Definitely start with the OEM ECU, that way you aren't getting into unknown territory (stand-alone) while also trying to debug other problems. Its much, much easier if you know you're starting with a fully functioning engine, wiring harness, sensors, injectors, spark system etc than trying to troubleshoot everything electrical at once.
I'm also a big fan of the megasquirt, especially for the DIY learning, but Kevin has certainly had issues with his which I'm sure you're aware of. If you want to learn (or at least aren't afraid of learning) how the electronic & controls side of the car works, I'd highly recommend the megasquirt, but it's not quite a plug-and-play sort of system. As an oddball option, there was also an effort on the RX7club to pull the processor off of the OEM ECU and replace it with a set of headers and flashable chip so that you can essentially be tuning the OEM ECU with all the control loops and whatnot that are already in place. The biggest downside there is the likely lack of support if things don't go well since its just a small group of people doing it, and the limitations as far as speed, table size, memory etc that go along with a chip designed in the 80s. Plus, for going NA to Turbo, you'd need to read up on it a little bit to see if you can scale the tables and change the limits for them, as well as use a bigger MAF or replace the MAF with just the MAP sensor altogether, etc.
Good job replacing all the freeze plugs - I had one pop out on me when I was back visiting my parents in NJ a number of years back, and of course it was one of the ones right behind the flywheel...