If running a double ground on the deck helped, I would do that. I had to do that an a EQ one time because the original ground wasn't good enough.
To answer two questions at once, if you get the distribution block, run a thick cable from the body to the block and you can run a smaller cable from the block to the amps(that is the way I have mine. The block that I have has one in for the main ground and four out. You can use two for the regular grounds on the amps and us the othe to for the ground screws on the amp cases and see if that helps.
I have all my wires and rca's ran down the pass side. I have my ground on the pass side strut tower. You should be fine on either side as long as your making a good metal to metal contact.
I just have my amps mounted to the back of my box. You should be fine with that.
Hope all this helps. I want to get the noise out your car as bad as you. Sounds like your just having engine noise now, so once you put the ground block on, hopefully it will take care of that problem. Let me know man.