Power vs manual brakes there is a difference in the pedal linkage under the dash. I can get you a pic of the power linkage later if you need. Manual just has a rod directly off from the foot pedal arm into the master. Maybe you are missing the power linkage for the pedal?

Concerning rear calipers, Those look huge, like they are front calipers. You will need to adjust the rear line pressure with the adjustable prop valve you have in the rear line.

Parking brakes -- are they in the caliper or under the rotor hat? If in the caliper, you need to hook up the cables and get the parking brakes to work.