pre-out noise

I'm assuming you've tried switching the outputs, as well as just running each pair on its own?  For example, give the 4-channel amp's front RCA inputs the signal coming from the rear RCA outputs of the head unit, and give the amp's rear RCA inputs the signal from the front RCA outputs of the head unit.  Try both of these on their own and then together.  See if the noise switches over to the other pair of speakers when you swap to different cables--if so, the problem is with your amp.  If not, then the problem is most likely with your head unit or with one set of the RCA cables (could be pinched somewhere or might have strands exposed touching metal somewhere in the vehicle).

By trying each pair of RCAs with each set of outputs, you are also essentially testing the integrity of those cables themselves.  Try all the different possible combinations and note any patterns.

Ideal way to troubleshoot this is really to just grab a brand new RCA cable and run it temporarily across the seats or outside the vehicle, from the deck to the amp.  If the noise is still there you probably have a problem with one of the components.

yea it sounds like you've pretty much eliminated the wiring as the cause of the problem...David Navone makes some really good noise filters, you might want to check out some of these, in particular the ones that say alternator noise filters.

It is possible that the ground inside the deck is messed up but I think this is very unlikely.  Even if that were the case, you'd pay more getting it fixed than you would on a good noise filter.  Just something to think about...