Hey, I had a 98 MM600 with the smart carbs and it worked great.
Your problem sounds very close to one I had a few times even after I cleaned the carbs. It wouldn't backfire, but there was noticable miss at higher rpms.
In the inlet throat of the carbs, there are a couple little holes that direct air flow to other parts of the carb/sensor (not sure on terminology anymore).
Check those passages very closely. There was a tiny piece of fuzz, that got sucked in there causing a partial blockage.
It did this a few times over all the years I rode it, but once I knew it was a simple fix.