No brake pedal

If we are to assume there is no air remaining in the system, the best suspect is rear brake shoes that are badly out-of-adjustment. Next, since this is a custom project, things to consider include the push rod in the power brake booster is adjusted too short, you are using a master cylinder for rear disc brakes on a vehicle with rear drum brakes, and the calipers' wheel cylinders' diameter do not match the diameter of the master cylinder's pistons, or there is an issue with the geometry or length of the brake pedal and its pivot point.

New disc brakes on all four, and all new lines. Booster push rod adjustment had been re-calibrated again. I am still very confused as to why, when removing the lines from the master and plugging the outlets, there is a good pedal with the first push. Thank you.

Different guy,

Maybe my approach will do something for you. Maybe not.

See "my answers" in this link.

https://www.2carpros.com/questions/1998-ford-f-150-cant-get-brakes-bleed

Return with news/ preferably good news!

The Medic

One thing caught my eye that I overlooked earlier. You said you plugged both ports at the master cylinder, then the brake pedal "only" went down half way. That is absolutely no good. You know it can only go lower when there needs to be enough fluid volume to work the calipers and wheel cylinders. With both ports plugged, the pedal should go just far enough for the lip seals to run past the fluid return ports going to the reservoir. The pedal should be very high and hard, and only travel about two inches.

Is it possible you have a brake pedal assembly that was meant for use with non-power-brakes? That will have a different leverage ratio to make the pedal easier to push, but it will require a longer travel.