For the most part, the 4Runner rebuild is finished. It took me just under 6 months and approximately $1500 to get her where she is today. She is now affectionately known as "The Avocado".
There are still some lingering issues from the roll that I will address over the next few months:
I have no headliner, and no insulation, which makes it very hot and oven-like.
I have no visors (need one clip to replace one that broke disassembled) and no center rearview mirror. I actually don't miss the mirror too much.
Still needs a roof rack.
Virtually all of the aftermarket electrical needs to be redone.
Small exhaust leak at the replacement Cat that will have to be dealt with soon.
So far everything has been working well. 4Runner did about 500 miles over the last couple of weeks, ~150 was offroad. Mechanically she is tip top.
Most of the work to be done will be recorded outside of this thread, except maybe the headliner parts, as that is directly related to the roll.
I would really like to thank all of you for your kind words and encouragement. It has not been an easy 6 months, but I am better for it, and in many ways, so is the 4Runner. I absolutely couldn't have done this without my very supportive and helpful wife. Alexus spent so many hours scrubbing, sanding, and prepping, not to mention kicking me out of the house and into the garage on days I didn't feel like working.