The fan temperature is not normally regulated by the ECU, is it? That is an independent temperature sensor, I believe.
I just looked at the wiring diagram for my bike, and the fan is connected to a temperature sensor and a fuse, but nothing connects to the ECU module.
A "chip tuning" will probably cause the bike to run a bit hotter, since it increases the fuel ratio and adjusts the ignition point, giving you more power from each stroke. (And generating more heat as a byproduct). This will certainly cause the fan to come on a bit sooner than on a non-chipped bike.
I know a lot of people "swear" by chip tuning, but unless you are going to go the whole 9 yards, installing a high-flow air filter, and replacing the entire exhaust system, the marginal difference of just a chip tuning won't do anything for you.
I've got a Timing-Retard Eliminator installed on my bike, the only thing that does "fool" the ECU into thinking it's always in 6th gear. Suzuki retards the timing in the first 5 gears to make the engine a bit "tamer" and reduce the emissions. I won't spend the money for a PowerCommander or other ECU enhancement unless I replace the whole exhaust system, and I'm not about to go spending $2500 on that right now...
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