I too have to lock my rear doors, then lock the fronts with the key. I replaced my front locks with a new Toyota pickup lock from Autozone- an exact match. I still get the hard-to-lock problem, sometimes they just don't lock. I always test by trying to open the door after locking.
Dome light: My switch was broken too, I replaced it with a normal toggle switch in an empty hole in the dash.
Windows: I have new felts, but my driver side door is tough to roll up. I can help it with my hand to a point, then it's very stiff. I've found that it can slip out of the side felt channels, when I push it back in it goes up a little easier. When I open up my doors next to coat the insides with CLR or rust converter, I'll take another look at the window mechanism, as well as take some photos. I do know that my windows is secure in the bottom bracket.
When cleaning out my tailgate, I successfully used rubber cement to re-glue the rear window back down into the bottom channel.