Sounds like a configuration issue. I've had issues similar to this on say volkswagon VR6 engines with the coils 'going high' or 'going low' (an option in the MS2) and dwell related... it often comes down to the coil settings in the computer.
This is the main reason I stick to Power FC L-jetro units for 500~rwhp sr20det or less. They are setup to work with OEM parts and do just fine... pretty cheap too... I got my last S14 sr PFC for $350 from ebay.
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