diode test the blown speaker and see if it is a direct short. Could have knocked something out of the output section of the "4 Channel" and the "mono" output is fine. Essentially it is 2 amplifiers sharing the same power supply so ignore the sub output when diagnosing. I am unfamiliar with the stock system however are you able to grab signal before the fatory amplifier? Sounds like a line driver issue and not the amplifier if so though I would be interested in buying the amp as I need parts for another rockford amp lol.
Do you have another amplifier you can test with instead? otherwise another thing would be AC volt meter the wires going to and from the LOC and when the speakers cut does the wiring to and from the LOC drop it? obviously probe the same speakers wires "+/-" then probe the RCA prong and shielding, don't matter what probe goes to what wire obviously with AC