The day I rode the bike home, the first thing I did was stop by a shop, swap tires and have them check over and lube the chain/sprockets, but I suppose anything is possible (stuck links, etc).
The feeling is similar to what I would consider "rough running" at those low RPMs, but it's not cutting out/missing and only
occurs when accelerating briskly and it does seem most prominent in the RPM range you stated. I've had Buells, 2 Honda Superhawks and a pair of Aprilias with 1000cc V-Twins and none of them felt this clunky down low. Granted, none of them, aside from the Buells, liked to pull away strongly at very low RPM, but the bikes didn't shudder the way this one does either.
I know this is sort of a hybrid between a "new" bike due to low miles and an "old" one simply from sitting for so long.
I'm still on the "break-in" oil. Getting ready to swap that with fresh semi-synthetic and put a new filter on this weekend (just over 600 miles on the bike now).
I strongly doubt the clutch discs are glazed.
Maybe I just need to ride it some more
I *have* been wondering if ECU mapping could smooth that bottom end out some, as well...???