Well I got 90% of the Noise out last night. I guess I will answer your questions first to explain. I twas a constant lound noise now it is a slight variating pitch noice. So I guess that is Engine Noise. Also I used the Adapter harness from Crutchfield to run everything. And I jumpered the Remote wire for the Stock Bose amp so that will turn on to run the 4" in the back and the Front Door speakers. The Pink Wire on the Stock harness. What I found last night was I checked the Ground on the deck and it comes out of the deck and goes in to the crutchfield harness and adapts to the stock harness and goes on from there. But then I took a piece of speaker wire and put it to the case of the radio and to a metal bar that is behind the radio and found that the noise went down to what I hear no. So then I disconnected the Radio Ground from the harness and found where all the noise was comming from. When I disconnected the ground that same noise was there I guess that stock ground sucks so I attached the speaker wire to the ground for the Deck and ran it to that bar behide where the deck sits and most of the noise is gone now. I still have a variable whine now but only from my 6X9 the subs seem to not have noise now. So for that I think I am going to make a better ground this weekend for the Radio just use some better wire I think I guess that is a good spot to run that ground too unless you know of a better spot.

Should I grond the Radio with the ground wire and attach a wire to the case of the Deck?
Question is the Amps have the Ground screw on the Case of the Amp Should I us it too? Can that be run to the Main Ground of the Amp to help things out?
Should the Amps Main Ground be run to a Distribution Block with short cables and then run to one shock tower with thicker Cable?
What side should I run the ground too my Power wire is on the POassanger side and my RCA's run on the drivers side?
My amps are also mounted to my box should I mount them to the Floor of the trunk or the Back of the seat?
I guess that is it for now let me know what you think and I greatly appreciat the help thus far