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I remember when I started my search for an ECU about a year or so ago. My head was spinning with all the terms and options when I tried to start researching. What finally helped me was a table someone put together summarizing all of the options and their capabilities. Not sure where that is, but I'm sure if you search you will find it.
To make sense of it in my feeble mind, I lumped them into categories:
-Megasquirt (MS Labs, MS PNP...)
-Not megasquirt (AEM...)
-Flyin Miata (Hydra)
-Piggybacks (forbidden)
I'm sure there are others out there that fall outside of these categories, but I eliminated them based on lack of support or capabilities.
I ultimately picked Megasquirt 3 by MS Labs. It's an amazing product in finish construction and capability. Unfortunately it's user (ME) isn't up to the same capability level as the ECU, so I'm having some problems with it.