Drive line noise mystery? Solved

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While you had the transmission down did they pull the clutch out for inspection?

Things I've found in the past.
Motor mounts worn or loose mounting bolts
Flywheel mounting bolts loose or sheared off.
Cracked flywheel housing.
Clutch housing loose.
Cracked center plate in the clutch
Rivets loose on the hub of the clutch disk.
Center plate dowels on the flywheel worn/notched, allowing the center plate to chatter or notched to the point of binding the disk.
Someone replaced the flywheel housing and failed to dial it to center. Which causes side pressure on the input shaft of the transmission.

Years ago I worked as a line mechanic for a company. One of the guys in the shop rebuilt a 10 speed.
He left a spacer out, which let the mainshaft move forward, almost an 8th of an inch. The truck made one 350 mile round trip, the driver told us of a noise in the transmission. Transmission was pulled and corrected. But the wear pattern had changed on the gears and the transmission had whine from that day forward.