Since it ran fine after u did the mods then it’s probably not the mods unless they created some sort of condition that fouled the plugs. Inspecting the plugs might give u some info.
Changing the plugs is a bit tedious but it’s really not that bad.
Ive only talked to the Nash guy once but he made a very good impression on me and he did LOTS of homework to do the flashes. I don’t think it’s the flash that’s casing the problem if u have the correct flash for your pipes.
Don’t u have to install an exup delete connector when u install aftermarket pipes ?
The symptom u describe sounds like maybe fuel isn’t getting where it needs to be quite right.
Im not familiar with the airbox mod but that could possibly effect fuel/air - lean/rich properties.
i would check injectors, fuel pump, etc., the whole fuel system.
If u always buy gas at the same place try someplace different just to rule that out.
I’ve run 89 octane (ethanolfree) in mine and didn’t care.