in the abstract I agree with your scenarios and our (hypothetical) perspective in them:

Imperialism would be our main enemy. As we fought the US and NATO, we'd very likely find ourselves in combat in which the Yugoslav army was our ally and the KLA our enemy.
But if the Yugoslav army and Serb paramilitaries were clearing out an Albanian village, we'd very likely find ourselves allied with the KLA and fighting the Yugoslav army and the chetniks. And if neither US/NATO nor Yugoslav/Serb forces were present, we'd probably find ourselves fighting the KLA to stay alive.

However, as far as I understand the situation, the whole process of "clearing the areas" in Kosovo has more to do with a military confrontation between the Yugoslav army and the UCK, then with expelling Albanians in and by itself. In the absence of NATO/imperialist intervention, we should probably be on the same side as the UCK, although that would also depend on what kind of area we would be talking about (for example, in a Serbian settlement, the UCK may very well be engaged in its own version of "ethnic cleansing"). However, given than any confrontation between the Voiska and the UCK is now part of a larger conflict, I can't see any possibility of being on the UCK side against the Yugoslav army at present.

Obviously, if there were any sizeable grouping of the kind I mentioned earlier -- a few hundred hardened militants... some of the best elements among the Serbian and Albanian populations, probably heavily working-class, perhaps with a strong component from Serbs expelled from the Croatian Krajinas -- they would have been fighting against the UCK from the very beginning. Given the political line that such a "Trotskyist multi-ethnic workers militia" would have been fighting for, the UCK would be in actual fact our main enemy, very much because they would think so, rather than the other way around.

To a nationalist, the worst enemy is never the oppressive power, but those elements among its "chosen people" who reject nationalism.

Your point about "political independence and an internationalist, working-class perspective" being crucial is entirely right. As well as the need for "tactical shrewdness and a lot of luck".