Microtech's ECU works in pretty much all the modern bikes. So yea, it will work in your 998 no problem at all. Contact The Duc Shop for pricing information. I think they're $1200 retail, but they may have gone up in price recently with the added import tariffs.
There is no benefit to running a 999 stock ECU what so ever. The gain in the aftermarket ECU is easy programming by the user and auto mapping, which is a great feature. The Duc Shop guys can talk you through the options.
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