| Never rode my 998R with the standard 50mm system so can't say what difference the 54mm makes.
Going on experience from a 998 I owned changing the exhaust did upset the running when on the standard ECU and fitting the correct ECU did sort out the running / starting issues.
Alternatives are to go for a Power commander or getting the stock ECU remapped by someone like Wilf at Moto Rapido
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