Here are some photos of the burned circuits. The links provided will access full resolution photos for easy viewing that can be downloaded if you want.
I did not attach the photos in the post as they might cause forum posting problems.
The wire @ the bottom (red on each end through a black tube) is the fuse link wire @ the battery. The upper red wire is the main power continuation to the switch.
The black wire with a ring terminal was the alarm system ground melted in half.
The other black wire is the switched power feed.
On a cautionary note to those that have never dealt with this, the best repair is separating the harness, removing one wire @ a time and checking all the other wires in the harness for damage. If I had not followed this practice I would have missed where the CDI shut down signal wire (blk w/ white tracer) had a bare area, that could have caused a problem later on.
Full size photo links:
http://aerox.us/roketa/roketa-burned-wiring.jpg
http://aerox.us/roketa/roketa-burned-wiring2.jpg