So you're saying that when the pedal is at the topmost position without being connected to the MC, the pin should line up with the clevis on the MC pushrod? Like I say, in my case the clevis is about 0.5'' off.

At the bottom travel end, it seems like the MC bottoms out about where the pedal hits the stop. I don't know if it's the piston reaching the end of it's stroke or something else on the MC stroke hitting something.