2nd to 3rd is grinding severely while standing on the clutch pedal?

Truck initially had a 5spd 4.3 V6 2wd. I installed a 2003 5.3L V8 using the original 5 speed.

From the get go shifting acts as if the clutch was not disengaging fully. It feels like the trans input shaft is rubbing on the flywheel. So, 2nd to 3rd is grinding severely while standing on the clutch pedal. Each shift takes no less than 3 seconds

I installed a new clutch, flywheel, pilot bearing, master and slave cylinder, clutch pedal, fluid, nv4500 trans, shims on throw-out bearing. I checked part numbers to make sure they were compatible. The issue has not been alleviated at all.

At this point I'm suspecting the 2003 5.3L crankshaft bore is incompatible with a manual transmission.