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Does it still pop with that harness disconnected?
What engine came in this?
Does that harness include disconnecting the high mount stop lamp if it's equipped?
Does this have a trailer connector? If so, have you disconnected or ruled out it?
Remove fuses #1 and #3 in the battery junction block and see if the fuse #13 still blows.
Ok, you should already know where the harness plugs in for the multi-function switch. Unplug it and see if the fuse still blows.
Other than that I believe you are going to have to be able to test where the high current or short is. The only thing is how since the fuse keeps popping. What I usually do is get a automatic resetting circuit breaker and attach some leads to it so you can plug it into that fuse 13 socket. This way you won't have to continue to replace the fuse. Then begin testing where the voltage is lost. It might be better though to use an ammeter in the fuse's socket, since the circuit won't be powered and it would give a better idea of the short because of the current reading being over the 20a the fuse is rated at.
The only thing is with the ammeter hooked up, you cannot really test, just disconnect things an see if the ammeter drops well below the 20a. I would try that first. Hook up the ammeter, press the brake pedal and confirm the ammeter reading is over 20a, then disconnect the multi-function switch and press the brake pedal again. If it remains under 20a, then jumper just the light green wire back, that is the wire that feeds that switch and then if ok, jumper back one at a time of the 2 wires feeding the rear stoplamps, they would be the light green/orange and the orange/light blue and step on the brake and see what the ammeter reads after jumping each of these. Jumping just so you don't have to hook the entire harness back up to that multi-function switch.
Here are the 2 wiring diagrams,