pan - first, welcome to the forums
I haven't looked closely at many v-rods, but if I remember correctly, they usually have a wide low profile tire and adjustable rear suspension. how does the suspension / air settings compare to the recommended settings in your service module?
As of changing the wheel, suspect you are going to have to pull the wheel and get all the specs - distance between sprocket & rotor (for line-up), rotor & sprocket bolt pattern, axle diameter, total width (for spacers?) . . . I believe the Ultras have had a wider tire for the last couple of years - not sure if they are as wide as the v-rod.
Then, if the circumfrence of the tire is significantly different you would probaly have an issue with the speedo . . .
Since the v-rod is such an "odd ball" and a lot of other harley parts aren't interchangable, I think I would personally try to find out why it seems rough first.
The first tool out of the box should be the "book"