Are you running the stock tune from the factory? Perhaps the changes you are making are enough for the bike to adapt to. What kind of gas mileage are you getting? If reasonable mileage is an important factor for you, keep it like it is. I made mods to my 07 Classic. DeCat, RamAir, TOR, O2 sensor Bypass+set-ON and HansO Tune. The bike runs well but mph is 25-26, no matter how I ride. The bike became very noisy. Recently, replaced one of the TOR for an OEM pipe. Sound better, same blasting ride.
If you want to try this tune, I think I can find the .hex for it. The 05 and 07 tunes should be compatible.
The need to mess with the bikes is an almost universal motorcyclist vice. Some bikes lend themselves to modding and the R3 is one of them. Some riders spend a lot of time near the red line. Some of us are lumper and ride in the 2 to 4k rpm range. The redliners benefit the most from mods. Us lumpers enjoy the smell of raw gas in the morning.