All fixed today, thanks again for the help.
I regrounded the amp powering the speakers with a single 8-gauge line to the same point most of the other guys here have and the whine went away completely.
I then regrounded the amp powering my subs with dual 8-guage lines to the same point, and changed the speaker wiring from 16 to 12 guage and OH MY GOD they hit 10Xs as loud and are CLEAN! At 50% gain my girlfriend heard it on the third floor of her condo and I was rattling her garage door in it's frame! I'm very happy now.
BTW, in case you're wondering I have 2 Boston Acoustics G5 10-44 Subs, wired at 2 Oms powered by a Boston Acoustics GT 2300 Amp with a 500 wt load to each sub. It's major overkill for this car but I love it
Speakers are Infinity Kappa Perfect 6.1 components powered by a Boston Acoustics GT125 amp putting out 125 wt RMS to each crossover. I would recommend a different speaker set up only cause the tweeters are dome and so I had to make a custom bracket to get them to fit in the stock location. But if you don't mind doing that they are great too. Crystal clear all the way up to volumes which make your ears bleed.