1) For USA Special Event #6, Jackson Bungling, does "defender" refer to a single unit or a stack?
The rating (leadership, not strength points) for the defending stack is "2" if it contains any Jackson units.
2) Likewise, for the Night March Special Events, does "defender" refer to a single unit or a stack?
3) Under Rule 8.6, it says *? means both sides may be Disrupted (on a roll of 1-2). Shouldn't it be just the indicated side?
No, both sides are Disrupted. The reason why the Defender or Attacker is indicated in the result is that, if the roll is 3 or more, it results in a retreat.
4) What happens if the alternative Manassas supply depot is also captured/destroyed, i.e. is that the last one, or does the Union player place another one to replace that one?
I'm 99% certain they're out of luck at that point, but I'll have to double-check with John.