Looks like everyone here has hit the major stuff.
I see you are thinking about removing doors.
My suggestion is half doors. No doors on a 4runner does not look good, like it does on a 40. Looks hacked and silly. Bill has a nice set of half doors, and you should be able to pick up a second set of doors at the yard for 50 bucks or so.
just my .02
Baby Beast 2- 1999 4Runner SR5
Baby Beast -1987 4Runner SR5-Gone, but not forgotten