I dont think anyone is going to be able to help you with very specific info from photographs. Electronics are the hardest thing to diagnose and when they have already been butchered like that its next to impossible. The only real way to do it is by spending hours and hours with a meter testing lines and flipping through diagrams.
There is no magic bullet for this stuff, with wiring like that your better off just replacing it all from scratch and running each wire by hand so you know.
Get a second car battery and hook it up with 2 leads. That way you can power certain aspects of the car without having the entire system functioning.
Also as Dmax said you need to know what was supposed to be there in the first place before you can repair it.
I hope you didn' pay much because this looks from the limited photos you've shown like a many thousand dollar fix.