The Basmachi have little to do with Al-Qaeda. They were to an extent "Islamist", but not of the modern kind codifed by the Egyptian Muslim Brotherhood after the end of Basmachi activity.
That is why I did not include them in the list but mentioned separately. However, they were a good example of Western support of backward Islamist (as opposed to Musavat, for example, and contemporary Tatar groups) movement. You see, although Basmachi sprung up from genuine grievances against Russian land grab, by mid-1920s (when British support piqued, although even at this point I wouldn't call British sponsorship a decisive factor) they turned into reliously fueled militant organization, preying on most medieval components of local social structure. Whatever educated local class was there either supported Reds (majority) or Whites, Basmachi were led by mullahs and tribal khans. So yes, in a sense it is an early example of using militant islam to hurt Soviets.
It should be pointed out that the political program of the Basmachi's Russian "Islamist" contemporary Musavat was full of references to Islamic freedom, solidarity etcetera, but it introduced universal female suffrage before Britain and America, so not every strongly Muslim political organisation is a bunch of fundamentalism whackjobs
Musavat was not RUSSIAN (it didn't even have sufficient base in Muslim areas of Russia proper, like Tatarstan and Bashkiria), it was AZERI. And they were not Islamist in modern sense too. More like Baath than early Al Quaeda.
I woud have to guess that the USSR would help with the Coalition and use it's overwhelming nmbers to squash Iarq. Afghanistan, though, they would stay out of.
I remember that noises about joining coalition were quite loud in Soviet political discussion in 1991. Although the support of USSR was almost zero at this point, so I'm not sure those ideas are not mutually exclusive. After all, Saddam was an old Soviet client and you don't betray old partners for no good reasons.
A more hardline regime might keep up the support for their puppet government, which OTL held on for three years after the Soviets pulled out [1] and collapsed in part due to the refusal of the post-Soviet government in Russia to continue selling them oil at discounted prices.
Even OTL Gorbachev regime propped up Najib to the very last day. So yes, any other more "pro-Soviet" regime would do at least as much.
it's possible that with continued Soviet support the government might hang on through the 90's, never actually winning but not losing either, and possibly achieving a compromise of some sort with the warlords and mujhadeen, especially if the US loses interest in funding them at some point or drops them for some Soviet concession otherwhere.
Yes, this is very likely scenario. I would dare to say that it is almost OTL development (what was known as "Northern Alliance" was a coalition of pieces of pro-Soviet pieces and some muj commanders) without keeping DRA badge and control over Kabul.
So, what happens in Afghanistan? Do we get a shaky Soviet puppet still in existence in 2009? A "coalition" government excluding those Taliban wierdos? Eventual collapse, civil war, and a Taliban takeover as OTL?
1st, this "shaky puppet" is more than Americans with their allies could achieve so far since 2001 (it is their piper dream to have Karzai as much in control of the country as Najib was). 2nd, I consider something between 1 and 2 most likely. Soviets started to draw "healthy elements within traditional Afghan society" (Soviet speak for groups which did not insist on public stoning of women for not wearing burqa and could tolerate infidels) in cooperation since 1983-1984, this tendention deepened by 1989 IOTL. So yes, I totally see somebody like Massoud sitting in ministerial office in Kabul under Najibulla.
In any event, Osama's ability to hurt the USSR probably isn't that great: I suspect it would be just a little harder to get a bunch of Saudi citizens with boxcutters aboard a Soviet airlines flight, and given Russians, there's a good chance they just get carved up with broken Vodka bottles.
You are right about hardships Osama would see in his attempts to strike USSR proper, but Russians with broken Vodka bottle isn't the main one. It was notoriously difficult for foreign agents to establish themselves in the USSR for a number of reasons, so Osama would have to rely on local groups (Chechens, Uzbeks, Tajiks, you name it). However, unlike American situation, when immigrant Muslim communities are insulated from mainstream American society (making infiltration very problematic), Soviets coudl rely on more loyal Muslim KGB operatives than whole Al Quaeda times 10. Any plan would be busted early. Besides, Soviet planes flew with locked bulletproof doors between pilot cabins and passengers and pilots were armed with handguns and knew how to use them. Shit still happened, but chances of getting half-dozen Muslim foreigners on the same flight would be slim, and of them having arms - even less.
According to some reports, Afghan government troops actually performed rather better once the Soviets were no longer breathing down their necks
Yes, it happened. And, to tell you the truth, I think it is pretty natural. Would you risk your ass fighting if there are big brothers with big... toys propping you up?