UPDATE:
Doing a data log with the engine not running but power applied to the Haltech and MSD is get
0
8000
8000
8000
0
8000
8000
8000
0
8000
8000
8000
0
8000
8000
8000
Hmmmm......
I'm guessing that the MSD is introducing some "noise" that Haltech is picking up and interpreting as RPM. The two boxes are a foot away.
Looked at the power supplied to both controller with an oscilloscope and didn't see any spikes.
Looked at the tach signal of the MSD box and is "square-ish". The wave form rams up to battery voltage, then there is a 0.5 volt dip for each spark, so the roof of the wave looks a little sawtoothish.
With an F7 Haltech, on can select the voltage level that the microcontroller will trigger on, which is 2.5 volts. The F3 Haltech has this capability built in so I'm guessing that 2.5 volts positive edge will trigger the Haltech.