Wow thats terrible.
Get some zip ties, if things are going the same way, stick em together.
Also dude, dont be afraid to damage wires.
If you see a sweet spot, stuff em in and get them nice and cozy. You really cant hurt them. Worst case a wire rips or snaps, just re solder it on, but I doubt that would happen.
Also the backside of you case is your freind. Run cables down the backside, and have them popup where need to be.
Think of it this way; I take a wire, and I ask my self, what's the most efficient way I can get this wire to that spot.
It's simple stuff.