I found a guy with an EcoBoost Mustang and he was having the same issue. Did all the same things… spark plug swap, coil swap. It ended up being a bad injector. I’m betting these are all an injector issue.
Yeah my next step is to swap around the injector. I'll have to find the torque values for the supercharger, because it will more than likely need to be removed. I might be lucky and just be able to remove the throttle body assembly, but I don't think so...
I have a 2017 Roush Stage 3. I took it to a very reputable performance shop and had it upgraded from Phase 1 to Phase 2, (pulley, fuel control module and tune). Shortly after I started getting P0308 and P0316. Changed the plug and swapped the coil pack with the #7 cylinder to see if the issue...