I did same swap last winter in my 95. 4.3 5spd to 5.3 5spd. You asked alot of questions. LOL. You also need the v8 motor mounts that bolt onto the frame of your truck. I used this fuel pump in my stock sending unit http://www.highflowfuel.com/i-478352...1988-1995.html
I used all new stainless braided fuel lines because the stock rubber ones from the tbi setup are to weak to handle 60psi. If your 5.3 is an 04, than it will also be drive by wire so you need the TAC module and the electronic pedal to. I made my own stand alone harness, and using a dual speed electric fan from the junk yard. From a Ford minivan. The stock 5.3 manifolds fit, but I went with schoenfeld long tube swap headers for 88-98. Your right about the pilot bearing and flywheel, the stock throwout bearing works just fine in my truck. I've beat the piss out of the nv3500 and it's doing just fine.