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And I BET #3 will soon be the 7AT flex plates breaking (I know mine has been broken for a good while)
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The flexplate/flywheel has the trigger wheel for the crank sensor. You said your flex plate is broken. I would start there. I've seen problems with no starts and hard starts with that.
If the ECU doesn't know where the engine position is, it may be firing the cylinders on the wrong stroke, causing your misfires.