first off.. u'r an idiot for cutting the factory harness.. with that said, it sounds like you have other un-related electrical problems with your car. The poping sound was probably your battery contacts just rejecting them selves, make sure that they are clean (wire brush if not), & make sure they are tightened securly (via wrench!).

hopfully when u cut the factory harness u didn't make one big cut, but u cut each wire individually. If not then you crossed a positive charge with every other wire in there even if the car was off due to the constant 12v power for memory!