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Are those backfires when cranking? Its cranks for a few seconds, then backfires, then cranks more? do I hear correctly?
I would start with the basics. Check compression. Check leakdown. THEN install all OEM equipment, factory fuel injectors, factory ECU, etc... everything back to stock. reset the ignition timing by eye and then with a timing light. Make the engine like brand new again. Make sure your injectors/rail is not leaking. verify fuel pressure.
Then, your starting issue should stop, and if not, diagnose that first before moving on to the misfire issue. they may be related.
if the computer IS already stock, i would replace that first.
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