After a bit more investigation today, and side-by-side comparison with a known fast 99 SM, found a couple things.
When full throttle, the OBD2 scanner shows the ECU is only seeing 86-88% throttle. The throttle body is wide open, cable is fine and also tried manually twisting throttle body. No change.
If I take the TPS off the throttle body, and use a flathead screwdriver to manually turn the potentiometer inside the TPS, it does register 100% throttle at the ECU.
Swapped TPS, throttle body, and ECU - no cigar.
I did notice the throttle body has "BP4W" engraved/stamped on it, but my ECU (and spare ECU that I tested) is a "BP5R". Is there anything to this? Different ECU's require different throttle bodies? (I find this hard to believe but figure worth asking). The reference Spec Miata that I was using had a BP4W throttle body and BP4Y ECU, and had no problem registering 100% throttle at the ECU. Unfortunately I didn't get the chance to try that car's ECU in my own car, got sick of the upside-down-under-the-dash work...
I was also told the 88% TPS did not matter, which would make sense if the air flow sensor controlled the A/F ratio. But in that case, what is the point of the TPS in the first place? I assume the TPS is an instantaneous tune change when quickly getting on/off throttle, then the air flow sensor takes over when it gets the information it needs. Considering the car did fine on the dyno, yet seemed slow directly after a shift or throttle application, does this mean I am headed in the right direction?
My car was showing some voltage variance (0.1-0.7 volts) at the O2 sensor, while idling.
The reference car had 0 volts at the O2 sensor, and actually never left open-loop on the scanner (mine said "closed-loop using O2 sensor"). I don't think the front O2 sensor was even hooked up on the reference car.
Curious as to what the O2 sensor actually does on these cars?
Sorry for the ramble, any insight appreciated.