I did not read all of this but will ask a simple question. have you tried a new coil? I have had two coils show similar issues at higher RPM, both from MSD.

Having said that here are some universal truths about MSD.

One, they have NEVER had a bad ignition box. Trust me I do not know of ANYONE who has ever sent one back and had them say it was an issue in the box

Two, Just because it is new does not mean it is GOOD. There is a difference. The digital boxes seem to have more issues than the old school ones.

Three, If you send in your old box they will send it back saying it checked fine but usually the issues you had will go away. Never understood this logic on their part but seems to be universally true. We have sen tthree back over the years with issues. All came back with no issue found and all worked great when they came back.

Fourth, They are very suseptible to RF interference. Factory tacks, electri water pumps, electric fans, alternator wiring or any other high current wiring will wreak havoc on MSD boxes.