This is the factory wiring from memory, don't worry it's correct, I've done way too many. Pathetic, huh?
Orange-Constant 12V+
Yellow-Switched 12V+(Ign./acc)
Black-Ground
Gray-Dimmer circuit
Brown-Parking light circuit(dims the brightness at night)
Pink-Antenna/Amp Trigger(if equipped)
Front speakers:
Left Front (+)-Tan
Left Front (-)-Gray
Right Front (+)-Light Green
Right Front (-)-Dark Green
Rear speakers:
Left Rear (+)-Brown
Left Rear (-)-Yellow
Right Rear (+)-Dark Blue
Right Rear (-)-Light Blue
That box in your dash probably was a line level converter(converts speaker level power to low level amp input power). I've seen many melt downs on the cheapie plastic ones as well as shorts, poor sound, etc. Audio Link makes a great reliable one w/ aluminum construction. I've never seen one of those go bad.
Don't worry about removing the factory wires if you rewire. Just don't use them and tuck the wires/plugs out of way. Secure them to prevent any rattles from the plugs or shorting and you'll be fine.
You can use a regular D cell battery to find the speaker wires in the dash. The speaker will make a little scratch sound when you send the 1.5 volts through it. This comes in handy to test for hookup etc and keep from getting the gray or yellow power wires confused with the speaker wires. While testing with this method, make sure none of the other wires in the dash are touching to keep from getting it wrong anyway.