Ok, well first off you should know that some vehicles require the factory radio in order to power other vehicle functions.... In some cases, you cannot remove or bypass the radio and instead have to relocate it. It is hard to see if you left the radio wiring harness attached to the radio itself and used the factory harness to attach your "new" speaker level output. If you did, you wouldn't have any problems... In other words, your radio should still be hooked up, but not the speaker + and - (those would be hooked up to your speaker level source) - if your using that blue remote wire, surely you must have the harness attached already.
As for your car... Disconnect your battery for at least 3 minutes (check manual for cpu reset times), connect your radio harness back to the radio and re-connect your battery.
As for the noise only do as I say if my assumptions are true.
I assume this is the order of your input series: pre-amp (soundcard) -> RCA -> input on amp -> speaker line level (+ & - for each speaker)
-> factory speaker wiring.
(no g-loop isolator yet) errr, remove it!
Try this: First thing to do is move a good sounding channel's rca to make sure that it is not the signal.... If one of the "good channel" rca causes noise in the bad channel's place, you can go from there. If no noise you may have a bad rca or input signal from the original source which caused the noise. If you still get noise, you would then want to swap the speakers that were noisy onto an already proven "clean" channel at the amplifier's speaker output terminals...
lemme know what happens
Good luck - and I hope the warranty covers