[INCOMING TEXT DUMP]
I hadn't thought much about the fate of the Yeniseians, but if I can get my hands on a decent reconstruction of Proto-Yeniseian with enough roots to construct names for people, places, and institutions in the timeline (I shouldn't need more than 1,000 roots) then I think that it could be very interesting to play with them ITTL.
I've provided as much information and reference as there basically exists on the internet, though if you want any summaries or information that's unclear from all that(it's not the easiest material to read and understand, for sure) then I can try to answer it. I've spent a long time reviewing the Ket and Yeniseians, for projects as well as simple interest. It becomes far more interesting than most people realize, especially their historical significance. You could call me a amateur Ketologist!
Sorry I couldn't reply more earlier, though. I'll have to expand upon some of the ideas I previously proposed, as well as some new variables considered.
I also hadn't thought much about this Sumerian beer-making cake method you mention. I've heard it mentioned, but I didn't realize that it was going to be a source of interest for anyone. I suppose since the purpose of this thread is to brainstorm, nothing is definitively set in stone for the timeline as of yet, so I shouldn't be shy about sharing my ideas here. Now, I had thought a great deal about Indo-Europeans picking up on the agricultural practices of the Caucasus, as I have been entertaining the idea of an early branch breaking off and heading south, absorbing the Maykop Culture and further moving into the Kur River Valley (modern Azerbaijan). From here, the expansion would continue along the southern coast of the Caspian and also onto the Iranian Plateau, which would absorb and displace Mannaean, Kassite (probably related to Hurro-Urartians), and Gutian-speaking tribes that would migrate into Mesopotamia during the early 3rd millennium. In this situation, I thought that the Sumerian city-states might play the different groups off of each other (Mannaeans, Gutians, Kassites, and Semites) to expand their own power, perhaps with a single city-state rising as the hegemon via the use of its non-Sumerian allies to some degree. I wanted to expel the Semites from Mesopotamia entirely during this period (sort of the way the Aryans were expelled from the Iranian Plateau ITTL) and drive them into the Levant at a time when clear boundaries between East and West Semitic had not yet been drawn, so that I can play with the evolution of Semitic languages and cultures to a degree during the Bronze Age.
Beer-cake making is just a slightly unusual cultural development that could be played with and modified in a number of ways to make unique dietary and social elements. Seeing how important alcohol and food storage has been throughout history, it's unfortunate that it is underestimated and underdeveloped. Your PoD and changes made creates a situation rather amenable to doing more with a rather novel aspect of early civilization. I'm rather surprised somebody hasn't done more with it before. The ability to ferment grains into alcoholic substances and use that as a preservative for food is easily applicable here, with a sufficiently high alcohol content placing cultural significance to breadmaking, and simultaneously solving food storage issues frequently encountered among the rural and urban lower populations of early civilization. If you consider how much alcohol is a social, cultural and even spiritual phenomenon among society, being able to adapt it into early yeast usage from beer to beer-gruel to alcoholic foods would be a rather original feature of Sumerian civilization, perhaps spreading to other forms of horticulture and brewing in time. Dry goods with alcohol exist via micro-encapsulation. By allowing the yeast to ferment in the bread and rise within natural heat instead of furnaces, you maintain both the dormant yeast for rehydration(complete with nutritional value), and incidentally allow the yeast to micro-encapsulate the ethanol if oil is added. In this way, dry alcoholic goods and seasonal fermentation could be developed in Mesopotamia, and then be spread further via cultural or societal diffusion. Interesting and maybe even strange results may occur: beer sediment breadmaking, alcohol-infused dairy goods, and literal sweetbreads with sugars in bread from decomposition of alcohol with spit(sounds weird I know, but it's been done before).
In terms of Semitic development, I did have a potential idea concerning their advent, expulsion and the collapse of Old Egypt, although it's slightly roundabout. If you start getting butterflies from that early on, North African affairs have to be considered with the environment of the time. Lake Megachad still exists, and part of the reason for it's demise- beyond the cyclical Saharan rainfall shifts and modern global climate change- is overgrazing for millennia and the extirpation of grassland-maintaining species that help prevent aquifer loss and excess infiltration. The region may act as a moderately populated region native to Chadic pastoralists and able to support a diverse environment for much longer if these alterations are prevented. If they can be by lower pressures upon the lake and more efficient land use, the region could easily maintain it's endemic wildlife much longer and even support civilizations that will enable further connectivity of Central and Sub-Saharan Africa with the rest of the Old World.
If Egypt is collapsed by Indo-European and associated migrations(I would love to see how that turns out culturally) and you have Semitic or Afroasiatic peoples moving further into Africa from the Levant or Egypt itself, I wouldn't be surprised if certain Semitic peoples migrate westwards to the Megachad region and settle in this attractive region. The diseases they may bring through contact with wider Eurasian populations and more urban settlement may impact native populations in a not devastating, but negative way. If you maintain conflict between the later Afroasiatic population and the Chadic populations, it may promote further societal development while limiting overpopulation and overextension of resources. Domestic grains such as watermelons, beans, sorghum and lentils would probably be introduced and naturalized further, as they adapt well to drought and flood cycles in semi-arid climates. The further use of agriculture to help create sedentary animal husbandry could promote the formation of early state entities in the region. Most fascinating would be what ends up happening to the second Afroasiatic migration into the region. It would no doubt create unusual linguistic and cultural features as an introduced group in the region. The closest equivalent to this idea in real life would be the Na Dene cultures, particularly the Navajo and Southern Athabaskan peoples, as a secondary migration of peoples into a region populated earlier by natives of a common origin. It would be one hell of a altlang, for sure.
Now, to my knowledge, according to the blog I shared, which according to my research is a good summary of the current status of the field of Indo-European studies, the period in question is the period of Common Indo-European, or what gets called "Proto-Indo-European" for people who don't understand the distinctions between say, Indo-Hittite, Graeco-Aryan, Northwest Indo-European, etc. So, the tribes migrating into Azerbaijan and eventually Iran and Mesopotamia are speakers of Common Indo-European, i.e. Indo-European after the development of contrasts in voice (it seems that at the time Anatolian broke off, the stop series was voiceless and contrasted for gemination) and aspiration. The Botai Culture, by this time, is already being affected by the immigration of the Indo-European-speaking Afanasevo Culture, and will only continue to be so as another branch of Indo-European migrates around the top of the Caspian Sea, only to break off into separate northern, eastern, and southern branches. I imagine that whatever language the Botai peoples spoke, it was the language that forms such a heavy substratum in Tocharian as to have loaned the majority of the nominal inflection, as much of that doesn't seem to be derived from Indo-European proper. That could still happen ITTL, but the Afanasevo Culture will be reinforced by a new wave of Indo-European-speaking migrants, so the substratum influence might not be AS drastic as it was IOTL. An increase of Indo-European migration into Central Asia however could definitely see an increase in lactose tolerance as well as the importance of horses during the period, as you suggest, though. But, when you talk about Western Europe, weren't sheep and goats already common by this time, and weren't they also being milked? I would be interested in your references there, cuz if dairy production came with Indo-Europeans, then Europe might not be well-known for its cheeses, which could have some interesting effects down the line.
Although the Afanasevo appear sometime slightly later than the PoD, your surmisation is probably realistic. Although various groups of the Botai may split off or remain unassimilated, any secondary waves may influence that substratum anyway. Horse varieties could vary and spread across Central Asia earlier. Paradoxically, the use of Botai horses as stout labor, diary and milk beasts rather than for riding could lead to more sedentary or higher density settlements in Central Asia, or completely new breeds designed for riding unrelated from those of OTL. The later arrival of modern horses from the Middle East and Iran could form a social revolution in a Central Asia structured this way. Either the contemporary horses are treated differently to the Botai ones(much like taurine and zebu cattle, or even like mules, horses and donkeys), and enable a transition back into a highly mobile, even faster nomadic society no longer reliant upon seasonal encampments, or alternatively this more sedentary Central Asia uses horses to connect regions and allow massive improvements in communication. Both outcomes are simultaneously possible, too- more prosperous regions like the Amu Darya and Syr Darya reamin connected settlements, while pastoral hordes remain like IOTL across the steppes, but having larger group sizes due to more efficient Botai-style grazing and herding. One possiblity is the greater cold tolerance of the Kazakhstan-originating Botai horses becomes exaggerated when someone brings them further north, resulting in Arctic horses like the Yakutian Cattle and Yakutian Horse(which are only 800 years old).
European domesticates such as cattle, sheep and goats existed at this time, and were used for making cheese from around 8500 years ago in Southern Europe. Over the next 1000 years that would spread to Central Europe and southern Britain. The irony of the situation is that cheese-making actually discourages lactose tolerance to milk- the bacteria long since broke down most of the lactose sugars. The concentration of lactose in raw cattle milk is up to 5%, whereas in cheese it is less than 0.5%. The reason why Southern Europe is less lactose tolerant than Northern Europe is that the region never developed cheesemaking before the Indo-Europeans arrived, and thus could drink raw milk only. The Indo-Europeans used raw milk as a staple in their cattle herding, and spread this genetic heritage with them. Old European cattle breeds were used mostly for meat and labor purposes, while sheep and goat herding was dominated by meat. Herd sizes kept pastorally simply weren't statistically large enough for dairy females to be a constant reliable food source, and group sizes weren't enough that you could specialize large numbers of people to managing hage herds in forest terrain best suited to fallow herds, not dairy management. After Indo-European arrival, raw milk consumption didn't explode overnight. It only becomes even a negligible part of common diets when enough forest is cleared and manpower is gained in the Bronze Age to allow large-scale agriculture and sedentary livestock maintenance.
Also, considering that it would seem that the Corded Ware peoples were not that into sedentary agriculture prior to the advent of Indo-Europeans, it might be the case that much of Europe remains in the hunter-gatherer (with some supplementary herding) stage for awhile longer, especially after the collapse of "Old Europe" (which is a subject I meant to do more reading about today). If that is the case, then it might also be the case that Europe is more linguistically diverse for a longer period of time, or at least that the form of Finno-Ugric that is adopted in Europe is rather different than what we know today, with a lot more substratum influence. It might also be the case that a mixed language between Finno-Ugric and some other "Old European" language develops and becomes the lingua franca of a new civilization, which would make things a lot easier for me, personally. The slowed technological development in Europe could give rise to the expansion of other groups as well. I had this idea of a Semitic thalassocracy of sorts developing in the Bronze Age out of Ugarit that would colonize places like Cyprus, Crete, Sicily, and the east coast of Iberia, but one that speaks something closer to Amorite, and not West Semitic.
If you let cheesemaking spread to Northern Europe as the world warms further and it becomes more efficient, then you have absolutely no need for lactose tolerance in Europe, and the region remains primarily hunter-gatherer and deeply forested. I wouldn't guarantee a lingua franca even forms in a region as divided, diverse and wild as that. Finno-Ugric peoples could move west and south easily, but completely extinct language groups could remain in many regions(I don't know enough about that subject to tell you what exactly). The possible closest analogy IOTL is West and Southern Africa, which remained hunter-gatherer and pastoralist within relatively unmanaged terrain, and despite that large political entities and foreign trading networks formed. I love your idea for a Semitic thalassocracy, and I'd imagine they work like Arab traders did with West Africa, perhaps spurring Swahili-style trading networks across Southern Europe, and the creation of native state-like entities. Slave trading may be a very substantial feature- there's lots of divided, small and primitive tribes to take prisoners from, and a range of river valleys and natural routes to take the captives southwards for easy trade via the Mediterranean. The high strength, foraging ability and natural prowess required simply to survive in a hunter-gatherer lifestyle may make them incredibly useful elsewhere within agricultural societies. I also wouldn't rule out Turkic or other groups migrating westwards along the contiguous Eurasian Steppe during a warmer interval to settle a relatively empty Eastern Europe, especially if civilization in Anatolia, the Caucasus or Southeastern solidifies more, as trade along the Dneiper, Volga and Danube rivers becomes more important.
As a side note, any thought or consideration of butterflies or interactions of the New World?