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Simplest way of answering that question is to get it diagnosed by a local indy or dealer. There are so many things that can affect running that make it difficult to diagnose over the internet!
We have found many issues with the Magnetti Morelli setup. It was not a very good ECM/Throttle Body Combination. We typically will go through the cycle of checking certain sensors but we highly recommend that if you want to keep the bike to strongly consider the Delphi Conversion Kit offered by Zipper's Performance.
2001 RK. No Low RPM power. New injectors new fuel pump new plugs--Could it be the TPS????
I'd suggest you take that to a knowledgeable, trusted, outfit in your area and have it throughly diagnosed to pinpoint the issue.
Those MM set-ups, can give good service, once attended to, correctly.
They'll never be a barn-burner, but that was not the intent either.
Scott