I had a horrible time when I replaced my MC and booster last year. Hopefully something in my story will help.
After the swap, with everything else unchanged, my pedal would get stiff and travel would become very short after a qhick drive. Ended up the front brakes also started to drag so badly that I couldn't even turn the tire by and after jacking it up. After it cooled down everything was fine. Pedal travel was adjusted all the way out but I couldn't give it enough not to run out of travel. I thought it was air in the MC, brake lines too close to headers, etc.
Read another post that ponted to some shoddy clearances between the MC and booster, specifically the rod. Ended up the MC was being engaging on me. Try this. Loosen the two MC to booster bolts. The MC should just sit there. In my case the MC wanted to pop off the face slightly. Nothing that made me think there was a problem. I threw some washers on the two mouting posts and I never had a problem again. Ended up the piston was being depressed slightly and after the brake fluid heated up I was getting enough engagement to drag the front brakes.
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