The early model ECM's before the overheat recall will have better throttle response in the lower gears due to more advanced ignition timing. Honda drastically neutered the ignition timing in 04 as part of the overheat recall campaign.
I believe what is happening to the ECMs is that the internal capacitors are failing as they age, and there is no way to open them up to fix them since they are potted. It's hard to predict when they will fail, but it does seem to be happening more and more. This is probably going to become the Achilles Heal of these bikes as they get older.