Odd master cylinder/braking issues

Manual brakes, I will check that for sure. Seems to me that it would have had issues earlier though. I’ve got 5000 miles on this build
Most likely not the problem than with manual brakes.

But it seemed that your issue has gotten progressively worse over time.

Professor Fate's auto adjuster thoughts are worth checking.

The MC could be sticking at the release end of the travel not allowing the fluid to go back into the rear resivour OR an internal leak from the front brake system to the rear brake system.