Ok, I think this is the last thing I'm confused about.
Can players capture strongholds with the +1 victory conditions? I'm pretty sure they can but want to clear it up before I move on.
yes - they are assaulted in the same way as cities.
If I still have living mercs on my stronghold, do I draw for deserters or are they all removed or do I do nothing? If they are all removed does this mean I permenently lose regular troops at a captured stronghold?
I admit this is not clear from the rules. My understanding would be that, since to Stronghold is removed from the game like in the case of a Noble's death, this is dealt just like a Noble's death. This means draw for deserters among mercenaries, if they have not been killed by casulaties, and keep your regulars.