loud thump when system cuts on

There are several companies out there that make a turn on delay circuit.     pac-audio.com      is one of them.  But to make sure this will fix your problem, remove the remote wire from your amp.  Turn the radio on, after it is on for at least a couple of seconds, then touch the remote wire to the terminal of your amp.  If the amp quietly comes on, this device will help you.

One way to eliminate noise is proper grounding and connections. I would recomend to not use the factory harness to hook up ground and power on HU. I had that same noise but it was when i would turn off my HU. The factory ground is more then likely connected to many other factory accessory grounds. When installing aftermarket products i would always recomend ground to the battery or isolating the ground from all other factory grounds.

might help.