Remote connected to deck? If so, maybe this wire is loose. If you are parked, hit the brake. If it goes into protect, then you need to do some electrical homework like you are saying. Review what has changed with the wires from your first set up to the second. Notice your deck and the instrument lights. Do they seem to dim more than normal especially when you hit the brakes?

Keep us informed
Rich

'96 Mystique, Zetec, MTX.
---Mods---
Removed both intake resonators and airbox. Installed APC air filter and APC crankcase ventilation filter. Removed exhaust resonator.
Installed XM Satellite Radio. Replaced bad alternator and 175a fusible link...much fun!
Intake plenum---GONE!!!!
My car growls louder than yours.
If I can't buy it, I'll build it...Trust Me!!!!