I have an 11 X and have done most of the blacking out you mentioned. Best bet is to pull off the grill and rear and take them in to get painted, or whatever you have planned. For the roof rails and window trim, I have come to the conclusion that the best way to accomplish that is to take the beast in to get those parts wrapped, and I will do that this spring. You can pull the side trim off easily enough, and I've seen black hood emblems but they were gloss black, so I left it on mine as is.
Here's a few pics of mine:
This Jeep has no name
PS-The lift I took to a shop, didn't want to mess with it and alignment, etc.