[buzzinhalfdozen]

Nice thing is you have a datalogger so you can rule out a few things, such as voltage issues as would be with a bad disconnect switch. Since it would seem you simply swapped engines (assuming you're using the same coil and ignition box tach ect.) I would start with engine grounds, crank trigger air gap, or simply swap out sensor. The polarity getting crossed on the crank sensor could be a cause as it would change your timing. Hopefully you have access to an MSD ignition tester, the first thing I would do is hook it up and run the system up thru it's range, this will let you know that the box and coil are up to the task. On the datalogger does it also show the RPM bouincing around also? Sounds more like you're having a triggering issue than anything. Hence using the MSD tester. Joe