Bad synchros, particularly for third gear, are common on these. That would suck, especially given your clutch nightmare. It would mean dropping the tranny again and either rebuilding or replacing. Btw, the clutch master is the one under the pedal, and the slave is the one inside the transmission housing.
Not entirely sure of your description, though--doesn't make the noise under power but worst in 3rd from 35-40mph?