67 twin turbo dart

True, was just looking for in site. They have sent the tune to megasquirt to look it over and see if he missed anything. When I was there we did log and send some to be checked over to megasquirt as well. Not really they are pretty much the only dyno shop that does megasquirt, all others are the more popular ones like your Holley. I know he kept saying it felt like the brakes were on when driving, engine revs clean he had been tuning that just to clear up the issue of the crank signal drop out which is taken care of now. Rev limiter was set to 6900 where I set it. Unless they did change it here's where I had it. Coil nominal dwell 3.5ms, spark duration 1.0ms. Here's the last I had for settings.

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I reviewed my setting compared to yours. Under "Ignition Options/Wheeled Decoder" I have "Ignition Input Capture" set to falling edge. The note shows this setting will correct timing drift. I do recall checking to make sure my timing was stable under varying RPMs with the timing fixed. I'm thinking falling edge may be the default because I don't remember having to change this to correct instability. I'd be interested to hear what others have theirs set to on their MS3.
I see their note says it was a mis-fire cut out. What was the timing doing during the cutout? Was it stable? If it was, the computer is doing its job and I'd look for a hardware issue. Plug wire, spark plug, coil, etc. Have you put a heat gun on each of the header tubes to make sure they are similar?