[RichardJ]

>>found a broken flare on the master cylinder side for the primaries.<<

"primaries" ? Explain. The rear piston in the MC is the Primary (singular). The line flair leaked and you replaced the line ?

>>Verified strong flow at line out of master, prop valve and out of prop valve. <<

If you cracked the fittings, pumped the pedal and got fluid out, when you released the pedal it would pull air back into the lines, combo valve and MC. Explain your actual process.

Did you recheck the booster pin-to- MC depth with the new MC ?

What bleeding method are you now using ?

If manual bleeding, I suggest getting a helper and open/close those speed bleeders as though they were regular bleeders. I'm not totally convinced your speed bleeders are acting as they should.