Before you removed the transmission for the second time, did the wheels move when you had the clutch depressed and the trans in gear (clutch not fully disengaging)?

Before diagnosing it as an internal transmission problem, I would try replacing the slave cylinder. The slave may not be working fully and is not allowing the clutch to fully disengage. It can also be putting slight pressure on the throw-out bearing, which could have caused it to go bad.

Also, how old is the brake fluid in the reservoir/clutch lines? Again, mositure and air could have gotten into the fluid and could prevent the slave cylinder from working properly.

Is the clutch fork bent at all?

My money is on a bad slave cylinder.