I had the same question. Here is what I found in one of Isaac Martin's book-
"...The reason is that the AOD transmisssion has a starting system connection in which, when the key is ON, in the START position, 12 volts are fed to pin 30 in the ECU connector plug. you can put the auto ECU in a manual transmission , since it doesn't miss the signal. If you install a manual transmission ECU in an AOD application that 12 volt power will fry the ECU."
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86 GT T-tops, AOD, B&M shift kit and hammer shifter, ROH wheels, K&N, Timing,MAC headers, 2.5 off road H, 2.5 American Thunder, 87 spindles, rear disc,SS lines, BBK 1.5, poly bushings, Crutchfield front kick panel speakers.
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