Shutter definitely not the norm, it "should" pull well from about 3k RPM.
There are a couple of things to check, most important is the inlet manifolds, that one hasn't kinked when they fit the airbox back up. It's hard to see and will cause this kind of thing. Next is the throttle body balance and the stepper motor. If it's missing, one of these is likely the cause, if it's not that, it could be a southbound plug, or a coil that's faulty or not fitted correclty.
If you're not happy with it, take it back and back and back until it's right, but if it's a big dealer, then you'll probably have little luck. You may be better taking it to a local indpendant, they're usually more careful and will find the cause straight away.
Perhaps find another 04 rider and see what theirs goes like?
JMHO
Mick