I used my neighbors reverse pressure bleeder to push fluid from the wheels back to the MC, so nothing was done to the MC. Figured it would fill up as needed and that was one of the purposes of the reverse bleed.
I would say the plunger rod I used was about 5 or 6 inches long. There should be no difference in adjustments at the wheels at all. Did you bench bleed the MC before bleeding the rest of the system? Don't preload the plunger by adjusting it so it starts the braking process before pushing the pedal. Just take the slack out. It's something simple. We are here to help!