Well. You are right the modify process for UDCs is not real good. Even switching is a pain.
You need the UDC files on the production server which you may be able to copy them directly to it and/or modify them as XML.
You also could create new ones and then convert them and have them created on the production site.
Probably best, once they are on the production site, is like you said to go into the manifest and manually change the reference, that way your bindings and things are not getting broken or needing additional work.