i screwed up, rca's, engine noise

I was hooking up my sub amp (Alpine MRD-M501) and I accidenlty connected my RCA's the the RCA out spot on my amp.  I didn't think anything was wrong because my sub was working.  After about a half hour drive I started getting really bad engine coming from my sub.  When I got home I started looking over everything and noticed my mistake.  I unplugged both RCA's and the engine noise went away.  I then plugged in one RCA (to the RCA IN this time) and there was no engine noise.  As soon as I plugged in the other RCA the engine noise came back.  I then tried a few other combinations and if only one RCA is plugged in there is no engine noise, but if both are plugged in I get engine noise.  I didn't have this problem until the mistake I made.  I even tried another set of RCA's and even swapping to the rear speaker RCA's to rule out a bad sub pre-out on the radio.

What could have happened?

No I have not.  Here is a complete story of the last week.

I had a Pioneer AVIC N3 to start with.  Wired to the factory radio harness.  Running a Pioneer 4-ch amp for the components and my alpine amp for the sub.  I didn't have any engine noise on anything ever.  I sold the AVIC N3 and installed my spare Kenwood HU until my new Clarion I ordered arrived.  The kenwood didn't have three sets of RCA's so I left the sub RCA'a disconnected.  I also disconnected them from the sub amp so it didn't pop from the RCA's touching something behind the dash.  I then installed my new Clarion radio.  This is when I connected the RCA's for my sub amp wrong to the line out preouts on the amp.  I drove the car for a half hour and then the engine noise started coming from the sub.  I did the above procedure in my first post and that is where I was last night.  I now have only one RCA plugged into my sub amp and it's fine.  Today it is 16 deg c out, at lunch I went to leave and I could hear engine noise coming from my front left speaker.  After the vehicle had warmed up inside the noise was gone.  I then tried plugging in my other RCA into the amp but the engine noise was still present so i unplugged it again.

On my new radio it has a black box on the yellow wire.  I'm guessing that it's a noise choke.  There was a lot of excess wire on my radio harness so i bundled it up and taped it around the black box.  Could this be causing some of my problems? 

I have 4ga power and ground running my amps.  I also have a 1 fared cap installed.  My ground is at a big seat bolt on the floor (paint scraped away and a star washer.  All the amps are connected to the same point.  RCA's are run down the opposite side the power cable is.

Like I said, I didn't have any problems with the AVIC or the Kenwood....Or even the Clarion until I connected the RCA's up wrong.  Is it possible I messed something up in the HU from connecting the RCA's wrong?

Should I ditch the factory ground and go stright to body ground on my HU?