94-95 MSPNP2 on a 90-93
 

So basically this is my issue, I have a 93 miata with a 95 engine, using 1.6 electronics as usual. I managed to pick up a MSPNP2 for cheap although its for a 94-95. My question is, how difficult would it be to change the ecu to work on my car or is it easier/more practical to just swap the 95 harness. Tried searching this up but only found results of the center connector being different or something.

Sell the ECU and buy/build one that matches the chassis. If you think you have the ability to change the pinout on a PNP ECU, then you have the ability to build an MS3+MS3x. You can sell the MSPNP2 for the same price as building an MS3x which will be far superior. There is no sensible way to change the pinout, other than making a jumper harness (which is ridiculous to do for a PNP ECU), and changing the harness is a pain in the ass too.

I'm running a 90-93 MS2 in my 94 Miata.
I had to swap one wire on the ECU harness to get things working properly.

Your results may differ.