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Newly rebuilt transmission with new input shaft. New clutch and pressure plate.

On startup after assembly, a rattling sound was coming from the bell housing area. Slight pressure on the clutch pedal smoothed everything out. I suspected insufficient lubrication on the clutch throw out bearing sleeve, and the pull back spring was unable to retract fully the bearing because of the tightly machined new clearances. I dropped the clutch cover from the bell housing to inspect with the engine running, but was unable to identify any obvious problem.

With the clutch fully disengaged, I sprayed graphite lube on the shaft and worked the clutch pedal back and forth. The rattling diminished noticeably, but there remains some noise (sounds like clunking and chugging, but not serious) coming from the transmission area.

The truck is now a bare chassis while I'm completing the mechanical portion of the restoration. Without body parts, sounds are obviously amplified. It's been years since I've driven the truck, and I recall there's always been a lot of gear noise.

Transmission is filled with Amsoil 50W. Any thoughts on what should be "normal" transmission sounds? Thank you.

The whine of the straight-cut gears is all you should hear-no rattling or clunking. You didn't mention replacing the throwout bearing-if that wasn't replaced I'd check it first. Also, is your pilot bearing in place? If not you could be getting some input shaft wobble. Since your truck is disassembled it wouldn't be a too-long floorboard bolt- that caused me much investigative work until I finally figured out what it was, years ago.
Please keep us posted,
Gary