Hello Ross,
Another option would be to measure the difference of the deeper set nipple and the rest.
Then place a washer type shim under the lower nipple. Of course depending on how much deeper the one is set, I wouldn't recommend shimming more than .100". Also you would want the shim to be tight on the nipple, not just a sloppy washer for this. I'd measure all and set the deeper one at the average of the five others. Of course if you don't want to mess with shimming or keeping track of a longer nipple, the only option would be to purchase a new cylinder. I believe a Pietta Cylinder can be cut down to fit a Uberti.
AntiqueSledMan.