if powerfc then it will be easy to see if ecuy has power.. as the hand commander will power or not.
Also on the 99 on the drivers side there is a plug near the air filter, if that is not connected fully the cam and crank triggers won't be seen by the ecu.
Also worth disconnecting and cleaning all the engine wiring looms like ones by the battery and one on the bell housing as it could be dirt in them
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