I've been watching this and just didn't have time till now. Shiner's thoughts are what kept bounding around in my head. He's dead on with dialing in the bell-housing hole to the pilot bearing. It's been a while since I've installed a std trans and it certainly wasn't in anything like our trucks, mostly hot rods, regardless I always install new components. IE: pilot & throw-out bearings, clutch liner and psi plate and resurface or new flywheel as well as fasteners.
FWIW - A buddy of mine had an 01, 3500, 4X4, QC/LB, 6 spd. he switched everything over to Amsoil. It was pretty hopped-up, he had Mach 5 sticks, twin turbos (non-gated), Drag Comp, head studs & water meth inj. I believe he had a double disc clutch. He never had problems with his trans., original to the truck.