So, after all the cranking tests I ran when I got back from Drag Week, and after finally seeing a solid RPM signal on the computer, and the alternately flashing LEDs on the ems-pro, I figured I had this problem more or less solved. The only bad thing I saw was that it seemed to take 5-6 seconds for the ems-pro to sync up to the sensor signal and start behaving correctly.
About a week after I posted that, Scott came out from under his Engine Masters project for a brief period and read my posts. He sent me an email that said the alternately flashing injector LEDs, which I had taken as a sign of success, were not actually supposed to appear until the engine started running faster than 300 RPM. During cranking the injector LEDs were supposed to flash in unison with the crank sensor LED. So, it appeared that I didn't have the problem resolved after all; cranking speed on the engine was only 105 RPM, so the LEDs should never have started flashing alternately like they did.
Scott suggested that I invert the signal from the VR sensor. This is a change to the DIP switch settings on the ems-pro, so was fairly simple to try. Today I hooked the laptop up to the ems-pro again, and after confirming the same behavior that I saw last time, reset the DIP switches to invert the VR sensor signal. Unfortunately this made no difference in the performance; the ems-pro LEDs behaved exactly as they did before, which is to say that the injector LEDs were flashing synchronously with the crank sensor LED, and the RPM signal was all over the map. Then, after 5-6 seconds the RPM signal settled down and the injector LEDs started flashing alternately. So apparently this is still not correct; what I'm looking for is the injector LEDs and the sensor LED to flash simultaneously, and the RPM signal to be steady on the computer screen.
In an effort to help the ems-pro see the sensor signal, I have acquired a 60 tooth wheel, shown in the photo below:
This wheel has two missing teeth in a row, and hopefully this gap will be more recognizable for the ems-pro than the single tooth gap that the Ford 36-1 wheel has. I'm going to try to get this wheel machined for fit and installed on the engine next weekend for testing. I was going to do that this weekend also, but getting my high riser project together ended up taking most of my time (see the new Member Projects board).
One other note is that I brought a Gaussmeter home from work last weekend to check for any teeth on the existing wheel that may have been magnetized. I did see some minor magnetization, but it was about the same magnitude as the earth's magnetic field, which isn't much, so I don't think this is an issue.
I should have another update next weekend.