Mutiny, desertion are punishable by death. 90 days is for federal service, state service can be until you age out so it was possible to request governors to keep those units on hand but as state troops, makes command and control more difficult but it would do as a stop gap measure until more federal units come on line.
This is totally unworkable. Quite apart from anything else, desertion might officially be punishable by death but it didn't prevent
enormous amounts of it happening anyway in the historical Civil War (sometimes more than a third of the entire Union army was absent); this particularly applies to units that are asked to do more than their official terms of service (because they're
not actually deserting, per se - they're going home in accordance with the terms of service for which they signed up).
Your remedy for this is for governors to arbitrarily extend the terms of units which consist of their voters! That's unlikely to fly.
The Union army
has more troops, it's called for five hundred thousand volunteers. The first 75,000 are going to say that if they wanted to continue to serve then they'd have re-enlisted, and they didn't; it's someone else's turn. This is why regiments literally march away from McDowell's army before the battle - they are going home to be mustered out of service.
Davis would have no choice but to flee as I don't see Johnston or Beauregard having what it takes at that stage of the conflict to keep a beaten army together.
If McDowell had thrown everything at once instead of piece meal, he could have shattered the confederate forces clearing the way to Richmond. Everyone at CWT keeps telling me if Richmond falls it is game over.
The problem here is that the army is fundamentally not capable of what you want it to do. McDowell knew this. He knew the army was green and not capable of an offensive campaign; his plan of action is about as good as it can be given the circumstances, because it at least avoids running head-on into strong enemy defences, and his campaign aim was to push the Confederates back to the Rappahannock and take pressure off DC - not to take Richmond.
And the way to Richmond is not cleared by a Confederate defeat at Bull Run. You have over a hundred miles to advance and you can't supply the army near Richmond; the Union army is not fitted out for an offensive campaign. Their only viable means of supply is down the rail line, but the Confederates have plenty of time to wreck the rail lines near Richmond (like, more than a week, in fact I'd be surprised if it's less than two).
"McDowell had hoped to have his army at Centreville by 17 July, but the troops, unaccustomed to marching, moved in starts and stops. Along the route soldiers often broke ranks to wander off to pick apples or blackberries or to get water, regardless of the orders of their officers to remain in ranks."
And you're planning on keeping this force together and win the war in one blow? Doubtless.
As for the "piece meal", where are you expecting McDowell to have pulled a drilled and effective army out of? This sort of thing takes time - these are his most disciplined and drilled troops and they're not very good because it takes a long time to make a drilled and effective army. The Union hasn't really exercised its divisions
as divisions.