brake issues, out of ideas...

While bleeding the system during the m/c replacement, the pedal would stop about 2 inches from the floorboard. I'm thinking proportioning valve, I'd appreciate any ideas or insight.
thanks

Edit you have manual brakes so this won't apply.

If you have power brakes might want to make sure the rod is inserted correct between the master and power boster. I only say that because I had a similar problem with the pedal not going to the floor when bleeding and I believe that was the problem.