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Unless there is something unique to the MSPNP, i would say it does not use the on/off switch TPS used in the 9093 miata. Which means you should be able to remove it no problem.
i believe matt came in here and said it does use the tps. I know on the 99 motor swap I have to move wires around on the 99tps to make it work on my 9093.
They may be using it for things like overrun, but on a normal MS build you can certainly run without one- I did for about two weeks while sorting my own analog TPS issues.