Thanks eth00...
Looks like it didin't need to do it after all via root. When I logged in I first took a look at the logs, and saw one of my clients had logged in via pure-ftpd just minutes before and was successfull. I ran a couple FTP log-in tests and it seemed to be working.
I went back to WHM, to tweak FTP and it showed Pure-ftpd was now being used.
Just not sure why to took so long in WHM, and never did actually see any type of success message.