The Megajolt system has a built in soft rev limiter which activates by setting the ignition advance to zero, greatly reducing engine power. This can be used even if the hard rev limiter is not installed. You can see the current value in the software along with the other settings.
One thing is to check the gap on the trigger wheel and the rigidity of the bracket holding the sensor. If there are any vibration that cause the EDIS module to lose sync with the engine, then a symptom similar to this can occur.
Another test is to remove the Megajolt from the equation. If you unplug it, the EDIS module will hold the engine at 10 degrees BTDC in limp home mode. The power output will feel 'flat' and reduced, but it should rev smoothly throughout the range; there shouldn't be any sudden dips in power. If you do, then the problem is centered around the EDIS installation.
Thank you, will watch for your updates!