Ok, here's the pinnout of the scanner port, as well as diagrams of the wiring for the port.
If you have any other questions please let me know. If you're happy with the information I've provided please click accept.
The pinout listing is color coded,
pin 2 is violet and yellow
pin 4 is black and tan
pin 5 is black
pin 7 is pink and white
pin 9 is link and light blue
pin 12 is light green
pin 15 is white and dark green
pin 16 is pink.
The only thing that will happen if you put them in the wrong holes is the scan tool won't be able to communicate, so don't worry about damaging anything.
The wire that was causing you the issues is the pci bus wire that goes in pin 2, if that touches any other wire or ground your pci communication bus goes down and you get the problems you had.
As long as all of the terminals are still on the wires you should be able to just slide them into position with no splicing needed.
Any other questions?
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