Well, I'll give you a break from my never ending supply of questions and give you some suggestions. I remember Alex and I were talking about the skinning of Kyle in Jabba's ship level. Kyle will initially start out in a white shirt with pants and boots on. Later, when he gets his gear, you may have a problem reskinning him in mid-level.
I think when you get to that little room in the middle of the dungeon control center where you're gear is, the level should end. Show a cutscene of Kyle pick his stuff up and then start the second level with the new skin on and with all of his gear.
Also once Jan is found, start a new level for that mission. Have a cutscene of their dialog that they exchanged, and then show them somewhere new in Jabba's Ship. Then start the level in a brand new area, so that you don't have to make a door to a new area.
This advice seems only to apply to Jabba's Ship, but I think for longer levels like this one and Madine's Fate, you may have to split the mission up into two or more levels. I mean I keep hearing something about a maximum model limit, and I will tell you that DF didn't have that restriction due that it was in 2.5D, that's for sure!

Actually, you can change skin or even model mid-level. Milesteg did some experimenting a while back, so that shouldn't be a problem :)

on some of the longer levels though we may want to split the maps up because they have a lot of those sprite stormtroopers

That's what the model limit thing you are alwa referring to is. Oh, I didn't know you could change skins mid-level. Oh well...