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There's a few things that come to mind.
1) What year is it? There were some in the early 2000's that had a shortened wire from the factory running to the front fuel injector. It would get tugged and pulled from engine vibration and eventually fail.
X) Fuel filter for sure, BUT.... also check the fuel pickup line in the tank. There's been many instances of them cracking and starting to suck air when the fuel level dropped.
17) The BIG one. Open mufflers, no air cleaner change? Has it had a tuner of some sorts, (SERT, TTS, Power Commander, et al) installed? If not, these pigs run lean as it is. If more air is going thru the engine than fuel to mix with it, it's gonna do a lean stutter. You're describing a flat spot. Common on carb'd bikes and lean FI bikes.
BB) Check the intake flange gaskets for leaking. Fully warmed up, at idle, squirt some WD-40 on the flanges. If it stalls, they're leaking.
That should keep you busy for a while. Report back, I'm curious.
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Meng
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