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.