Brake pedal is really stiff

The M/C will get toasted if the pedal goes down too far. Hmm, you mean the seals inside the bore might get ripped if the travel outside the bore in a rough casting ?
That's how I was trained. Never go past 1/2 way when bleeding or seal damage will occur. I'm not an expert but Consider my mentors and teachers to be among the best so I just always did what they taught me no questions asked. Back In the day we just stuck our left foot under the brake pedal and pushed till we hit it lightly. About 1 1/2" or so max. My bet is still on the Prop valve, or Wrong Shoes, Or improper installation of shoes/Hardware.
I don't believe we even have enough to go on because we don't know the full sequence of events that led up to the problem. Or even how the brakes were before the Brake job.