Glad I'm not the only one with this exact problem. I have a similar set-up: Woodstock HU, Fosgate comps in the front, fosgate amp in the boot powering a JL 12W6 sub and the front comps.
The Woodstock HU uses an external pre-out wiring harness the same as the oem units with 2 sets of pre-outs with 1 common ground. I built my own signal cables with expensive twin screened cable and connectors.
I stripped the whole of the interior to lay down the cables ensuring they where well away from any sources of interference or snags.. I'm on my 3rd re-wire now after trying everything in the text books to resolve a major hum/whine/hiss in the system.
Sent the HU back for testing.. came back fine.. they sent out an electrical engineer to have a look.. spent a few hours over looking everything to no avail. He suggested just running the front comps of the HU, which I've been doing for a few months now and it's fine. But this is only a cheat.. the front comps come alive when run through the amp (tried in a different car, works fine)
I recently learnt/read there's something weird with the mk4 grounding.. something about a split ground between front and back chassis??
I've now been redoing the ground connections in the engine bay, HU and amp and checking the resistance through the chassis to find a solution. This weekend will be the final straw!!
Hopefully feed back some useful info soon!