Extreme injector 3.5 wont open

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This once again brings me back to the ECM. Neither my OTC or SnapOn scanner will clear the code, neither will a hard battery reset. Not an injector or coil code, but a P0304 #4 misfire and the code will not clear. One more thing, the vehicle has a still has a hard code for a #4 misfire. Does anyone have any ideas, suggestions, or diagnostic advice?

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I suspect that shorting the wiring during diagnosis has fried the computer, but I am not completely convinced especially knowing that the vehicle ran before repairing the injector harnesses. I have rechecked the wiring repair, and even with the repaired injectors unplugged the vehicle will not start and I do not get injector pulse. After repairing both harnesses the vehicle will no longer start, and has no injector pulse, but it does have spark.

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While inspecting the wiring with the vehicle off there was a spark from some of the bare wires and thought perhaps there was a 'pop' sound from the engine compartment. Looking under the hood I found rats had chewed through the #4 injector harness as well as damaging the #6 harness. My Highlander was running rough and had a #4 cyl misfire. I'm having a problem with a 2011 Toyota Highlander 3.5L.

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