Aside from the hardware differences/issues of building one from scratch, most of what you need to know/learn you can figure out by installing the MegaTune/MegaTunix software and playing with the interface. It is a fairly standard ECU.
I am hoping to swap a running motor in that car sometime in the near future.
Once that is done I'll need to tune the ECU for the:
a) actually decent condition motor not about to spin a bearing / reciprocate itself to death
b) slight bump in compression (shaved head)
c) uhm, ignition maps, yeah, uhm...instead of the Flyin' Miata Link ECU base maps that were translated over to the MS
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