I work in water rights from the technical side. I know how important water rights are, and how confusing they can be, but it seems a little bit of escalation has occurred here.
I think your first post is a bit contradictory. If the current land owner conveyed water rights to you, that he believed were conveyed to him and all of the property was researched, then you are the current water right owner, you just need to straighten out the chain of ownership transfer.
The first thing to understand is that a water right is a property right. They are dealt with similar to that of other property rights. A quit claim deed could be a way of processing the transaction, but, as suggested, a property attorney or water attorney would be advised.
Do you know what kind of ownership interest is held in the ditch? For instance, is it a mutual ditch company, carrier ditch company? Do you own a water right or do you have a contract to receive water?
I don't know what part of the state you are in, or what the water right is. If you are in the South Platte River Basin, that is Division 1, Division 2 is the Arkansas River Basin, Division 3 is the Rio Grande, Division 4 is the Gunnison, Division 5 is the Colorado, Division 6 is the Yampa, and Division 7 is the Dolores/San Miguel. The senior priorities in each of these divisions are of different vintage. South Platte Water Rights usually have an earlier date than say a Colorado River water right, though they would be of similar relative priority. For instance, the controlling right on the Colorado River is the Shoshone Power call that is a 1905 priority. A 1905 priority on the South Platte would go out fairly early in a drier year because of the number of much earlier irrigation rights . So knowing the relative priority of your water right and the relative location of the water right in the proper division is informative.
For a little more reading, you might check out this brief article by Ray Petros: http://www.cobar.org/docs/WA040706J-01-0607191.pdf?ID=1475
If you want to check out more information about your water right, I can either talk you through looking up information from the Division of Water Resources, or you can go and play around on their site. Just send me an IM if you are inclined.
Not sure why the link is not active. It is a colorado bar association link.