42Miata

Hello all, been trying to figure out a minor issue and want to make sure I haven't missed something obvious, or made a mistake in my tune. I installed a MS3Pro PNP into my 2000 SE about 2 weeks ago and have been having some success getting it tuned and up and running. Right now I have 2 small problems, the first of which is that while tuning using VEAL, often no changes will be made with all of my driving being filtered due to "Idle VE Active". Even when doing a WOT pull to 7k RPM it is all filtered due to idle ve active. I found a workaround while trying to troubleshoot this on my own. If I open the Engine States window in tunerstudio, autotune immediately begins working as expected. It still filters idle out if idle VE is genuinely active, and tuning while drive works well. Is there some small setting somewhere I missed? Is this a software bug? Is this indicative of a sensor issue of some kind?

I drove the car for about 500 miles (the car is new to me) on the stock ecu and everything worked perfectly, no issues. Since installing the megasquirt the car will sometimes start rough and sound like its running on only 2-3 cylinders. Cycling the key in the ignition (car off, and restart engine) will fix the issue most times, though I occasionally have to restart the car 3 or 4 times for it to run correctly. This issue so far has only occurred at idle, on my last drive, while tuning the car on E85, I drove around for almost 30 minutes without issues, then while sitting in my driveway with the car idling it just lost 2 cylinders and died. It restarted without an issue and ran on 4 cylinders again. My troubleshooting on this issue is limited as the car really doesn't want to run when the issue is occurring, revving the engine sounds brutal and I have too much mechanical sympathy to try to keep it running when its rough. When the car was on a 91 oct tune, it would idle rough without dying, I managed to pop the hood and start pulling plug wires, I pulled cyl 1 and no change, reconnected. I pulled cyl 2, and immediately heard the sparks arcing to the head/valve cover and reconnected it and the idle was fixed. This was the only occasion I was able to resolve the rough idle without re-starting the car. Now that the car is tuned on e85, it will not idle on 2 cylinders and just dies when the issue occurs, limiting the troubleshooting I can accomplish.

I believe it is likely a coil issue (I probably had the key on, engine off, for extended periods when initially setting up the megasquirt.) I do plan on replacing the coils with the FlowForce R8 COP kit within a few weeks when I do injectors and a fuel pump to prepare for turbo, but wanted to see if you guys might have other insight. Should I be replacing the CAS as well?

EDIT:
Replacing coils fixed issue, and turning off VSS detection for idle in the engine states window fixed the VEAL issues.