When all fails, usually its best to start again from ground zero. That means disconnect everything and connect one item at a time and test, then hook the second item, test and so on.
The trick part of troubleshooting is to keep it simple, look for the obivious( look with your eyes open, sometimes you tend to get wrapped up so far into troubleshooting, taking voltage and so when it could be a simple switch setting on amp, wire connection, loose wire, headunit settings and anything.
but in your case no wiring or euipment ever changed, just doing big 3 wires and shorted the positive wire to ground. It seems you tried everything.
So maybe how about if you undo the big 3 and return system back to normal before big 3l. And see if system works, if it does, then big 3 is the problem. And then troubleshoot. troubleshoot one item at a time.