If I understand correctly, you made the rear AC Zone 1, added 12V to it and ran the thermostat directly to the back AC and the rear AC ran correctly.
Did you then try and make the front AC, Zone 2 and reinitialize?
Try that. If you get the E01 code I believe you still have a communication cable issue between the front and back units. Can I assume you used a communication cable and not a phone cable?
If you have the proper cables, did you replace the small cream colored connecters that connect the communication cables to the AC harness?
Are all communication cable ends in like new condition. If not, clip them off and install new ends.