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Did you break open the other ecu to check for burnt pins or anything? I had this same issue a while back with my RB. The kid that wired it up left a bunch of open connections and shorted out the ECU. It ran great, then it all went to shit. Then would be ok for a few. Then go back to shit. I pulled the harness, rewired it, put a new ecu in, and it's been good ever since.
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