Bhull1985,
I have done a similar thing - apart from the last step. Have a script to run to set up other users with the enterprise cuix. The shortcuts and Ctrl+click appears to override the main cuix and work from the installed custom enterprise cuix fine and as expected. This is kept in central location, so updates are automatic for others.
The only reason for enquiring about partial cuix loading in the shortcuts is because sometimes we use third party software loaded into AutoCAD which can have a Enterprise cuix associated with them. I believe only one enterprise cuix is allowed. I have a separate desktop icon with a switch for a different profile and load in the enterprise cuix as a partial cuix in this instance.
Thanks, Robbo.