Closing this thread with my results
Problem #1: Drivers side door gap.
Solution: A new latch assembly fixed it. The curved ridge piece inside the latch had worn down over years of use. Fascinating how these things actually work. Getting the old latch and screws out wasn't fun, but I'm glad its done. Picture below is the section that was worn out. When the door closes, the ratchet action doesn't hold so that let the door pop out the 1/2" or so.
Problem #2: Drivers side window won't go down
Solution: A new window regulator went in and went nicely. Lesson learned, take out the 4 clutch bolts and replace them with machine screws. I spent an hour trying to get the window back in with the track still attached to the bottom of the window frame. The right way, is to install the track into the two rollers of the regulator, then insert the window. Line up the holes and install the machine screws. So much easier!
Problem #3: Passenger door won't open from the outside
Solution: Mostly, I'm an idiot. Turns out there is a setting with the inside door handle where it locks the latch. I replaced the door latch because the inner door handle was falling into that position after a few bumps down the road.