This is my first post on here and wanna say this build thread is amazing. So glad you stuck with the 2.5 too. I just picked up an 86 MJ with a 2.5 so this is a huge inspiration. Keep up with the updates.
My buddy used Speeduino to tune his supercharged Miata and it seemed to work really well. There isnt nearly the same support as megasquirt but after the initial setup it's pretty easy. Neither one of us ever tuned before and we got it running pretty well.