Yes, clean the torque tube and slide the bell/ball/cover and all parts/seals/gaskets as far back as possible.
If/when you buy a clutch assembly kit (clutch, pressure plate, release bearing, pilot bushing) it might have a pilot/alignment tool. That can be used to check the fit of the pilot bushing.
Before you install the clutch assembly, make sure the pilot bushing in the end of the crankshaft is good (will have a tight fit against the "snout" on the forward shaft of the transmission). Replace bushing if it is scored or makes a loose fit.
You would then install the correct clutch assembly inside the clutch housing (inside the clutch/bell housing, which will have the clutch release bearing arm attached inside).
You could then do the gasket/seal adjustment procedure outlined in the post above.
Then, install the u-joint assembly.
And, finally, close and tighten the ball joint cover.
Do you know anyone nearby who has worked on these trucks?