Need some help replacing ecu harness

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You will need to disconnect the ECU in the passenger wheel well, then snake the wiring out a small hole in the firewall. It was a PITA when I did it for my Cobra conversion. The engine harness is in 3 parts (if I remember right) - what part do you need to replace?
 
I was running the A9L computer but I want to put mine back in and get it tuned. But Iv hacked up the old harness pretty good so I just need to replace the 60pin wiring that plugs into the computer.

I just want it clean with no splicing down there anymore.
 
Ah. That harness runs through the passenger fender and plugs into the the other harnesses in two spots:

* Passenger firewall, in the corner: plugs for the engine & transmission harnesses
* Under the air filter: two plugs connecting to the fuse box harness

The same ECU harness runs to the CCRM and fan as well. It's certainly do-able but it's still a PITA. It might be easier to pull that part of the harness out, properly repair it and re-wrap the harness so the splices aren't visible. For a new harness, try eBay or your local junkyard.