Sorry for the delayed response - I'm out in CA preparing for engine masters and in the middle of my own "Jay-style Thrash!" :-)
OK, so here is how the fuel pump is supposed to work, in software:
IF you have a "priming pulse" greater than zero, the fuel pump control powers up (grounds the relay) for 2.0 seconds. IF the priming pulse is set to 0.0, you will get NO fuel pump relay control when the ignition is switched on. That's the only thing that controls the "ignition on" 2 second pulse, or not.
After the 2.0 second pump operation, the EMS turns OFF the fuel pump until the RPM is greater than zero (engine is cranking, for example).
Jay, what I noticed in Topeka was, looking at the LED's that light to indicate tooth pulses being seen on the Tach Input, the EMS seemed to be "resetting" at cranking speed. What you should see when cranking is LEDs flashing consistently, but yours would flash 3 or 4 teeth then stop. This explains the fuel pump not being commanded on.
A good way to test this would be to put the wheel on a drill press or mill where you can control the RPMs carefully, and see why we are losing sync at the roughly 125rpm your engine was cranking at.
I checked with the software developers, and one thing they HAVE seen is on high compression motors with missing tooth, wasted spark setups just like yours, is that the missing tooth might be happening right after a compression stroke where the RPM is changing dramatically as the engine is cranking (after all, the actual RPMs when cranking vary a lot, more so with high compression). They suggested that the missing tooth period is happening too quickly so that the timer that measures the period between crank sensor teeth, isn't able to detect it until you hit higher cranking RPMs. I believe them. They suggested re-indexing the crank wheel so the missing tooth is farther advanced than the 45-50 degrees you have it set at now (BTDC).
Unless something changed in the behaviour since topeka, I'd focus on what I believe is the EMS not "syncing" with the wheel. Although, MANY people run this combo and don't have the issue you do (Bill Fowler, Brian Rock, both with high compression engines as yours, BUT I noticed Bill's cranks around 175rpm). I am pretty sure the behavior you are seeing with the fuel pump is a result of the EMS not being able to sync up and count rpm properly, at your cranking RPM (i.e., the fuel pump behavior is exactly as expected). I think the software differences are just that - configuration differences (priming pulse set to zero?)...
What I plan on doing when I get home is testing this on my engine simulator, with the trigger wheel mounted to a variable speed drill press, now I know that the EMS will sync at low low RPMs (one guy with a radial engine cranks at 35rpm and is able to sync up fine, but it's a low comp engine)... and I'll run your MSQ file on the same version of the box to be sure.
NOW, that being said: we HAVE seen "firmware corruption" and I can walk you through a field reflash of your firmware. I have seen it happen usually with a "spark event" (jumper cables creating spark, or shorting out a starter wire by accident). This is NOT the same as reloading your "tune" it's actually a firmware reflash and worth doing.
I get home Monday and will be on this issue like flies on stink!! I cannot stand having anyone with confusing issues, we'll figure it out. Hopefully what I typed above can help a little in the meantime?
Talk to you soon,
-Scott