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The disc that came with mine would not work with Vista so I called dynojet and thier website has a place to download the Vista program. I did that in about a 1 min download and all works well.
I emailed Dynojet about Windows Vista, haven't heard back yet (weekend). So it's good to know that it will work with my laptop. Think I'm going to get a PCIII from fuel moto soon.
If you think Stage 1 is all you will want to do, I personally would just get the ECM flash. If you think your plans might get more ambitious later go with the Power Commander. My tech told me it's cheaper and easier/faster to tune with a PC than the SERT.
Since the ECM flash reportedly costs ~$170 and the PCIII around $280 from Fuel Moto with an accurate map for your bike, why waste money with the former? Closed-loop mode will be unaffected by the flash, so running at stoich (14.7:1 A/F) the bike will still run as hot as it did in stock form. There will be some improvement in performance due to the opened-up intake and exhaust, but not nearly as much as with a Fuel Moto setup.
BTW, to the OP: Consider Fuel Moto's Power Package (AC, PCIII, and Jackpot mufflers). It may be the best bang-for-the-buck performance upgrade available for stock bikes.