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YES...you need to adjust the INITIAL TIMING by disconnecting the wire lead that takes the ECM out of the equation and then reconnect it when you are done.,...and YES...the ECM does adjusting timing but you have to have the initial timing correct
BY disconnecting the wire lead for setting your timing...your CHECK ENGINE light will come on and you will need to clear the code when you are done.
AS for the timing light...using a timing light with the advance feature helps out....and I would also suggest that you do not ASSUME that the notch in your harmonic balancer is correctly positioned and has not spun....thus causing any of your timing efforts to be in vane due to the notch has moved.
I would set the timing as needed and if it seems to not be right...then that is when I would verify the notch is correct or not.