I think maddogcycle is right. One cylinder is running rich and the other running lean. It seems as though they have not been balanced properly and the mixture not accurately adjusted. The settings on these carburettors are critical and must be adjusted with the proper gauges. I'd advise you to have the carbs cleaned and adjusted and tuned to the engine for balance of inducted air flow and fuel/air ratio (mixture)
Sounds like one of your sensors is going like the TPS Throttle Position Switch this sensor samples the distance of pedal travel to the throttle cable travel then compares the two signals calculates the preset number that is sent to computer module. The switch is anchored by two screws the adjustment there determine correct signal.
Either your coils are bad, or they are not getting power, or they are not getting a signal from the pulse coils.
Check ignition fuses
Check for ~12V at coils with ignition on.
Find pulse coil connector, check resistance across leads, should NOT be zero, and should not be infinite, consider about 100 ohms OK. (These wear out more often than the coils.)
If these three checks are OK, check the primary and secondary resistance of your coils. The resistance across the wire connections on the coil body should be about 10X the resistance from the spark plug wire to the coil connection.
All the best!
