It sounds like you have a problem with the clutch linkage assembly (clutch cable, fork, pivot) that is complicating the adjustment, and causing other problems, such as the failed throw out bearing... I don't think that you necessarily need to rebuild the transmission.
What manufacturer clutch cable is installed on the car?
Is there a aftermarket quadrant and firewall adjuster? If so, what kind?
I'm assuming that the clutch fork and pivot ball are original and came with the transmission?