An observation I made with my engine is the ignition system is wasted spark, opposed to the COP used on non VVTi 2JZGTE engines. Thinking more about the cam and crank trigger arrangement, it seems that it would a bit difficult to interpret sequential fueling and ignition from this arrangement due to the evenly spaced cam trigger.
Looking at the trigger logs above, one engine cycle has two cam pulses and another cycle has a single cam signal. Being that these signals are so close to the missing teeth on the crank signal I could see how the camshaft changing timing would cause this pattern to invert, in the sense that one of the pulses crosses the missing teeth causing the cycle that had only a single pulse to now have two pulses and vice-versa.
Seems that even for Toyota, this was a potential issue. I don't have wiring diagrams available at the moment for the 2JZGTE VVTi, but I'd imagine the fueling was batch fire as well if the ignition was wasted spark, with this particular arrangement.
88 RX-7 TII - MS2 Extra 1.0.2
68 Mustang 351C - MS3X
88 Volvo 245 - 2JZGTE VVTi powered, MS3X + MSGPIO Mshift controlled