... Doesn't ECU flashing involve a dyno and a laptop and then you build a custom program based on the performance and real world output on the dyno specific to that car?
I believe I've read of other people's engine swaps involving the ECU from the donor vehicle that the engine was pulled from... Now, I could be very wrong and you could probably have someone go through the effort of flashing your current ECU on your YJ - though if I were you I would do some research into what possible ECUs you could use. It might be a lot cheaper to go and pull one from a U-pull than it would for you to re-flash your current ECU..
This can be a BUMP
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