Thanks for the replies beltfed and Grigg,
I got the master cylinder from the older corvette, where the rod goes in is much deeper. I put it on and set up the rod a little bit different. Bled the brakes and went for a nice long drive and they never got hot at all.
So I don't know if it was the linkage or the m/c but either way it works and I am cruising!
Thanks for the help!
So for future people searching this thread. If you want manual four wheel disc brakes, use the 68-76 Corvette Master cylinder.