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I'd be very careful about changing the transmission out. The ECM has a turbine input speed sensor and the differential speed sensor. If they don't match, it will freak out, declare the gear ratios are incorrect, and run in a limp mode. As far as lean burn, you may want to look into Sniper or some other ECU reflash software so that you can program the actual fuel tables to be lean where you want them to be. Therefore no trickery needed to fool the ecu.
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