Worth the hassle?

This Jeep is posted on CL http://twinfalls.craigslist.org/cto/1518920530.html

I've got a 96 that has more than it's fair share of issues so i'm parting it out. Would this 99 be a good donor? Take the 4x4 from the 96 and swap it into the 99?

How tough would a tranny gasket be to fix and the door issues?

I'd say it's worth it. You are going to want to be lazy and swap the entire transmission from yours into it anyways (though I think there might be input/output speed sensor differences? hopefully lawsoncl or one of the other good transmission guys on here will pop in and answer definitively) due to the tailshaft+tailhousing/cone differences between the 2wd and 4wd models, so I doubt the seal will give you an issue. Depending on what seal it is, it's not too bad... front seal = drop tranny (doing anyways for 4wd conversion) pop the torque converter off and pry the seal out, replace.

Door issues I bet are the door check bar, maybe 30 minutes to an hour of work and less than $50 with brand new parts if I'm guessing right, definitely under $50 in junkyard parts.

Window issue is probably a broken wire somewhere in the flex duct between the door and the body, not a big deal to fix. Do it at the same time as the spring issue while the trim is off and you'll be fine.