I wasn't quite clear whether you bled the new MC's you installed. A new MC does need to be bled. Some MC's come with a fitting & rubber hose to bleed the fluid back into the MC; then follow the other member's suggestion of getting any residual air at the top of the line where it connects to MC. If all air is out of lines then it sure sounds like the pads are too far from the rotors causing the need for a second pump. Even with the two person method stubborn air bubbles can be hard to move to wheel cylinder / calibers for bleed off. A high pedal with the engine off is normal, even with an incomplete bleed. Again, make sure you've bled the MC properly in all reservoirs.