There is something missing in this story. Cakewalk overwrites rapture.dll during the install process. It seems like there were attempts to manually merge VST directories and rather than overwrite files, the copy process was told to copy but retain both files. If the "middle rapture...comes up ok", it would appear the valid installation is the rapture(2).dll. This is because by default SONAR orders plug-ins alphabetically by folder, by plug-in name. This would lead me to remove rapture.dll and rapture(3).dll. If this works, I would rename rapture(2).dll to rapture.dll.
If the delete and rename does not work, you might be able to get away with removing the 3 dlls and run the X3 installer, take the advanced install option selecting Rapture from the pick list. If that does not fix it, there is a more elaborate process to perform a clean install. But let's see if one of these options works.