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It sounds like an issue with the coils. One thing you'll want to do is take a data log - with MegaTune, if you hit the space bar, it'll mark areas of the log for you to come back later and look at. Check to see if Megasquirt is losing the tach signal at the same time things are breaking up. If you're losing the signal there too, check for a noisy crank trigger. If you're getting a good RPM signal on the log, suspect the coils or the coil driver circuit.
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