Although I own a Megasquirt ecu and am having a problem with EMI interference, I have dealt with this problem with Microtech ecu's and I know that Haltech and other users of different ecu's encounter this problem from time to time. Although my question in this thread is pretty basic, you can read alot more about my problem in detail here:
https://www.rx7club.com/megasquirt-forum-153/what-can-i-do-avoid-misfiring-756611/
So, all in all, my question is more aimed at aftermarket ecu's with this problem. I've dealt with and tuned 2 Microtech ecu's and 3 Megasquirt ecu's that had this problem (some worse than others---aka: my car) and I've read about quite a few Haltech users that have dealt with this. I've been searching and reading up on this problem ALL DAY and I decided to post a thread on this subject because I didn't find a good enough answer to this problem after searching on this site, nopistons, and various other sites.
So, anyone care to share?

 

Many times it always got to do with the install.
If you have tried everything else then you could change the trigger signal from a reluctor/magnetic type to a Hal Effect signal. That would only work though if the interference is actually effecting the trigger pickup. Some times it's elsewhere.
You got to narrow it down to the source of the EMI intereference.
Removing likely sources would be a start.