Uninstalling is not going to affect the registry. If you are going to re-install Rapture, consider using the installer provided as a standalone for X2
http://www.cakewalk.com/Support/kb/reader.aspx/2007013294 .
I would also not mess the with data stored in c:\ProgramData. It does not take that much space and is the only hidden portion of Rapture.
As far as the portion that default to "C:\Program Data\Cakewalk\Rapture" for some reason, the new installers ignore the rp registry entries so you can either continue to move expansion packs by hand or forget about the registry when relocating the files and use mklink to create pointers to the new locations. For that matter, you can skip the re-install and create the appropriate links now as if you had installed in the default location. That should be sufficient for future expansion pack installations.