I have been having an issue with my R3T. When it's under load all seems fine but when the load is off (e.g. cruising at low speed with more or less not load such as through a slow zone or rounding a bend, or cruising at motorway speed with a strong tail wind) the bike runs rough. I surges and feels like it's missing or wanting to accelerate. It's no fun to ride.
The dealer changed the Throttle Position Sensor but it did not fix the problem. I checked for any pinched or blocked hoses to the Mass Airflow Sensor, cleaned, crimped and grease (dielectric) and reseated the coil wires. The problem didn't go away. It turned out to be the GI Pro unit. When I installed the unit (GI Pro w/ATRE) I set it to the recommended setting of "3". The problem disappeared as soon as I ran it on the setting of "-". Same issue on a setting of 4. So the unit works fine as a gear indicator but it would seem I can't use it for that power boost.