I also have a Cobra with a bowtie motor and like you, I was faced with a similar mess when I first looked behind the dash. In fact, that was one of the major factors in my decision to disassemble and rebuild the entire car with new parts and wiring.
One of the best parts of that decision was the purchase of a completely new wiring harness from my car's manufacturer, Unique Motorcars. I got a complete harness made for Unique by Prodesign Systems and for a complete novice at automotive electrical wiring, installation was a snap - far easier and safer than trying to muddle through the mess of wiring that I'd inherited.
Here's a schematic diagram I drew up a few years ago when I was doing some troubleshooting. Its based on the actual colors of the wires used and is drawn from a combination my own tracing and the schematics in the Prodesign manual.
Hope this helps
