Wow really long time since I did an update. No lack of work going on. This will be a multi-parter.
After I got the motor running I tried to get the alternator working. It was originally computer controlled and the megasquirt has a provision for this. Unfortunately it didn't work for the RX-8 alternator. This was after doing hundreds of dollars in damage to the electrical system of the car. The alternator just went full bore and was trying to charge to over 100 volts! I started the car and noticed the voltage was a bit high and was creeping up towards 18v. Then smoke came out of my lithium battery and the car sputtered and died. Turns out lithium batteries have little tolerance for over voltage and will fry themselves. Then after the battery fried there was no capacitance in the system the voltage sky rocketed and blew up the ECU, both of my wideband controllers and damaged my motogadget control unit(start circuit stuck on). Luckily a friend of mine after more than a few hours was able to repair the ECU. The battery was covered under warranty by Battery Tender. Can't say enough good things about those guys.
After several back and forths with megasquirt and testing with a lead acid battery in place I couldn't get the alternator control to work. Plan B was to install a 1991 RX-7 alternator. That is internally regulated and worked with almost no modification. I only had to drill out one tapped hole and swap the pulley.
Next up is brakes!
RX-7 Alternator in place-
Some of the ECU damage. This was the only obvious thing blown up. There were about a dozen components that needed to be replaced.