Wow, what an endeavor. I am working on My 83' FJ 60 as well. I am trying not to complelely disassemble it, at least as far as you are going. I only have a 1 car Garage and the Cruiser won't fit in there anyway, so it's in my Driveway and the weather is finally warming up enough to get things rolling.
Problem is, I have a lot of the same issues that you do, especially fender rust. Right now I am working sort of from the ground up. I have replaced all of the Suspension, Including springs shocks Ubolts and Bushings, and will be doing the shackles and pins soon. I have also rebuilt the Hubs on the Front. I will soon be rebuilding the Knuckles and replacing the brake calipers with 4-runner calipers at the suggestion of folks on Mud, followed by a Clutch rebuild, and exhaust replacment. I am trying to de-rust, clean, and paint everything I put back on the rig. Once everything is sound, Mechanically, i will begin doing body and interior work.
Do you see any problem with Rebuilding a 60 without taking the body off of the frame? You at least have convinced me that i need to take everything off of the front, as you did, to really access the Engine. I want to eventually pull it to rebuild it but time and funding are limited.