you really should have had it on a dyno when you first put the ecu in, you dont know how lean or rich it is. It could be running way lean causing the flat spot and pinging too. Then again it could be running way rich at that point causing the flatspot, either way you should have had the AFR's checked by now. SAFC should be zero'd out with the new ecu too.
The o2 sensor can cause bad fuel economy, you could always disconnect it and monitor fuel economy.
Bookmarks