the main reason for not removing the handles or rear bumper is actually just time constraints. I have to have the jeep done and out of the shop by Thursday since that will be the end of this phase, (aka almost like a semester here) I have been pulling double shifts of class (550am-7pm) for a week just to get to this point I'm at. As for the door jams I masked them off with the doors on, future plans for the jeep are to actually restore the interior meaning mainly the floor. I am going to bed line the floor and at that time I will be changing the door jam color, as for right now however the biggest concern was fixing all the rust and getting it painted.
My Amber Fire XJ Project: http://www.jeepforum.com/forum/f22/amber-fire-xj-rejuvenation-project-1048331/