Did you use poplar or non-polar caps? If you used polar, there is a chance you wired then in backwards.
Re-bundling wires can help sometimes, but it usually is not the cuplrit people make it out to be...
Where is your radio power connected to the boat's electrical system? Over the last 6 or so years we have deteremined that for the quietest noise-free installation, your head unit needs to get it power at the same voltage potential and ground plane as your amps, and the easiest way to do that is to wire your head unit's power wires, (red, yellow, and black) directly to your largest amplifier. From the factory, most head units are wired into the helm wiring and often even on a different battery from the amps, and this is a very common cause for noise.
Your yellow wire needs to go straight to the +12v terminal of your biggest amp. The black needs to go to the ground terminal of your amp. The radio's red wire needs to go through a switch of some sort. Many times, we use a 30A relay which allows us to use the old switch power lead, (the old red one) as a trigger for the relay. That way, you can can turn your head unit on and off the way you used to. IF by chance you have a simple switch at your helm that turns the radio on and off, you can just disconnect the wiring from it, (taping it off or removing a fuse to prevent a short) and use the switch on a new run of red power wire from the qamp, through the switch, and to the head unit.
I have attached a couple of non-schematics, (actually pictures) that show the twop options I describe. If you did not re-wire your head units power when you added the amps, this may very well take care of it. I have also added a 3rd pic to show the use of a 30A relay when three or more amplifiers are used. Many times, the turn-on circuit of a typical radio will not have the oomph to drive 3 amps, os it is often a good idea to use a relay to get power to the turn on connectors of the amps.
Outside of re-wiring your head unit power, understand that the very condition you describe of hearing lots of noise from all accessories is a very common symptom of gains being turned way too high. Please check your gains again, if they are over half-way up, you probably have an issue. Ideally, you want your gain controls as low as possible, not the other way around...
Good luck, study the pics,ask questions, and let us know!