Two more things to look at. One basic, one not so much.
When you adjusted the rear brakes, you were sure that the parking brake was completey off, correct? If not, that would definitely mess with things.
The fact that the pedal is firm when the engine is not running says that your pedal-to-booster rod is adjusted pretty well, and that the booster is good. Just make sure that if you hold the pedal down, the booster doesn't release too quickly. Should hold a hard pedal for quite awhile if I'm not mistaken.
However, the fact that your pedal goes way down when the engine is running could mean that the booster-to-master rod is not properly adjusted for the new master, or that the new master is not correct for the booster.
That and the bench-bleeding issue are both very important.
What disc brakes are these? Ford or non-Ford conversion? If a kit, or something that you put together yourself, can you see daylight between the caliper body and the knuckle?
To check, poke your head in over the top of the tire and look down at the front edge of the calipers. If you can see the ground between them, you're ok. If not, you didn't grind enough material off of the steering knuckle to clear the caliper and it's binding.
Good luck. Sorry if some of this was discussed already.
Paul