Just play with different maps........................I can't see not being able to tell if it's a shudder or a sputter though.

A sputter would be under acceleration, a shudder would be at certain speeds (balance/alignment issues) or while braking.

When bikes have been messed with (aftermarket exhausts and the like) they can sometimes get a dead spot. And some bikes can have a dead spot stock from the factory (mine did) and getting a jet kit or PC can help cure that.