Wow, you've had more than your share of teething problems with the new parts. The brake setup that you have should work okay with a manual master cylinder. If you want to debug it you might start by verifying the brake line pressure at both ports on the master cylinder. Verify that the rear port is feeding the front brakes. You could have a bad prop valve so bypass the prop valve and any other valves in the system. Another way to tackle the debug is to verify brake line pressure at each wheel. That test will show you a kinked line or a stuck prop valve or something like that. A super cheap test is to just put some marks on the rotors with a felt pen and see if all four brakes are working. What you describe sounds like either the fronts or the rears are not working which would point me towards a bad check valve or a bad prop valve or a kinked line or something like that.
I felt that something was wrong and I may have stumbled upon it.
Today I got the manual MC out and the booster in. As I was bench bleeding the 1 1/8" MC, I noticed that the front port got the fluid first and the bubbles first. The rear port only started pushing fluid about 1/3 the way into the stroke. Usually, the front port serves the rear brakes while the rear port serves the front.
With the brake lines connected the traditional way, the REAR is getting pressure before the front.
This can't be right.
I tested a stock iron 15/16' MC and front and rear get pressure at the same time.
I tested the Dr Diff aluminum 15/16" MC and it was exactly like the larger 1 1/8" version: Pressure and bubbles at the front port before the rear.
There was no tech sheet in the box with these master cylinders but Mancini Racing includes this sheet:
