I have to ask. Where is John Young in all this? From my understanding in or time line he still retained active flight status as a Astronaut up until his retirement in 2004 even though NASA never assigned him to a mission after STS-9. I think in this time line after ASTP II he kind of disappears. However based on him sticking around in or current timeline I really don't see him leaving NASA. He was kind of bureaucratically banished after his pointed criticisms after the Challenger explosion but that never happen in this timeline. If he is still around he would be a excellent source of knowledge from his experience of Apollo 10 and 16 and he is probably the only active duty astronaut that would have experience of actually landing on the Moon.
He's probably been flying, like you say I doubt he's left. However, I've been aiming to use non-OTL astronauts as much as possible since I can put words into their mouths without worrying. Of the 64+ missions to both Spacelab and Freedom that have happened ITTL by 1996, I've covered a very limited number with full crew counts. Young has probably flown once or twice more to either Spacelab or Freedom in that time, but is by this point probably mostly of the active list and into supervisory or training roles for new astronauts.
First, I'd like to thank everyone involved for writing and illustrating such an interesting timeline. This has become one of my favorite things on the internet (even though I do grieve this universe's loss of the OTL Star Trek movies and later series).
Well, thank you very much for your kind words. I'm always glad when people enjoy this as much as we enjoy working on it.

Also, I see it's your first post, so I'd like to also take this chance to welcome you to the board.
I'm really looking forward to what TTL does with some of the modern/planned missions like MESSENGER, Stardust, Genesis, Hayabusa, Rosetta, OSIRIS-REx and Solar Probe Plus. I think you've also got a prime opportunity to try for realizations of Cassisi/Galileo class Uranus and Neptune orbiters as well as a properly realized JIMO/JUICE set of orbiters for the Jovian moons and maybe even a slightly more ambitious TiME.
I tend to leave unmanned planning to Workable Goblin, so I can't offer a definitive answer, but we're both pretty excited about future missions ITTL. I know we've given some attention to the potential for Mercury and Uranus or Neptune orbiters, and to missions to some of the moons of Jupiter and Saturn, but I'm not sure exactly what's topping the list of likely to fly at the moment--besides, that would be telling.
I've got some questions about some (relatively) small details.
I'll try and get to the ones that Goblin didn't, then.
It also seems that the Russians would upgrade one pad at Site 250 for Vulkan and keep using Site 31 for any remaining R-7 launches.
Yeah, Site 250 is for Vulkans, and site 1 and 31 were in use for R-7. However, with the decreasing use of those for anything other than national defense payloads and the breakup of the USSR, most R-7 launches have headed to sites inside Russia proper, so both Site 1 and 31 were semi-abandoned. After the Gararin's Start fire, Site 31 is the only remaining R-7 pad at Baikonur but mostly inactive (though in slightly better repair).
At the Cape NASA obviously has both LC-39 pads for Saturn and I'm guessing the Air Force upgraded LC-37 to handle their Saturn launches. So I guess Lockheed would get LC-40 or 41 for their commercial Titan (is that still running btw?) with the other getting rebuilt to handle Delta 4000/5000 (unless they rebuilt LC-36 or one of the other Atlas pads since these Deltas seem to be TTL answers to Atlas III and V).
Titan is indeed still running at LC-40/41. (That's the topic for a post a few weeks out.) LC-36 is the Delta pad, and Saturn ops for national security uses are at LC-37.
At Vandenberg I'm guessing SLC-3 or 4 is used for the Deltas while SLC-6 would built to handle Saturn?
Something like that, yeah.
- How do the umbilical towers work for Saturn Heavy? Obviously the central core has its tower which can be used for Medium launches but with such little clearance coming out of the VAB high bays do the booster cores have short towers or has Multibody switched to using tail service masts like OTL Delta IV? Also, would NASA keep using the unwieldy Mobile Service Structure that had to ride on the crawler?
I lean towards tail service masts. These can be more easily set up so the boosters can be identical instead of mirror-image, simplifying construction of the cores.
- When the Soviets switched to TKS for manned flights would they have kept using the old SSVP docking system from Soyuz or take the opportunity for a larger docking collar (and thus crew transfer tunnel) like the hybrid system on ISS?
It's a solid maybe. There's benefits in a bigger hatch, but they got by on OTL Mir with the same hatches as on previous stations, so presumably there's a strong legacy reason to stay with it--you have to convert all the equipment on the ground, too, and potentially re-engineer the DOS modules more. Because IOTL they didn't switch to hybrid until ISS, I think they might still be using SSVP unless someone makes me a very persuasive case for it. Anyway, what I can say is that Salyut 7, Mir, and Longxing all use the same port, whichever it is.
As I said, awesome timeline and I hope you keep it going past modern day all the way up to a Lunar base and manned Mars missions (at the rate you're going you could easily beat the OTL 2030's plan).
Thank you, and once again I'm glad you're enjoying it! However, we're looking at ending the TL at about 2014 with the end of Part IV (essentially, we'll bring it to the present day at the time that we finish it, and stop). Partly this is because this TL takes a lot of work and time, and we're sort of interested in working on other projects, and partly it's due to the accelerating issues of planning alternate technical developments. As we go further beyond OTL's tech level and explorations, we start to get to the point where things get very speculative on a tech level.