What CDI system did you replace (specification of it and matching coil) and what condition was it in?
I've tried every inductive ign snake oil out there and nothing comes close to matching a M&W proDrag2 Hi/Lo combo, you will need x 2 of those boxes and their latest CDI coils and it wont have the issue your 'tuner' says it has
It's an ignition misfire cause its incapable of running a true water injected car,
tune the engine don't let it tune you