There are literally no owner serviceable components/systems on that motor. There are some fault codes that when they occur and are stored will not let the motor run more than 1200 PM.
The EMM does control everything including the injectors and also monitors and controls the fuel flow rate through the injectors.
Your symptoms sound like a bad injector.
I'm starting to think the EMM is the weak link in those motors. I have a 2015 90HP and it just had an EMM replaced at 240 hours for a bad voltage regulator.
You didn't say what dealer changed the EMM, but Chris at Action Marine is about the best etec guy there is. Aaron and his guys are top notch.
2015 Seaark 1872 MV CC Etec-90
Two Helix 12 CHIRP SI's, , MinnKota Riptide ST80/i-pilot Link, Bob's Hydraulic
Bitter Gun Owner