You'll probably have to do it the old fashion way...
- Trace each wire to its source/destination
- Determine if the wire is needed
- Look for a better way to route the wire
- Shorten the wire if possible
- Safety tie the wires along the way to mak'em look neat
To determine if everything in your mess is needed, I'd start by Googling for the install manuals on all of your aftermarket components; then compare what you got to the wiring diagrams.
It's not 'fun' but I'm much the same way as you when it comes to wiring...trust me, you'll 'feel better' once you've got it all worked out. As a side note; I've never found an installer that didn't create a mess of wires, that's why I just bite the bullet and do all my installs myself.