While working with the same client, the existing jQuery worked perfectly and would replace any "http" references to "https", and modify the URLs to either use the short or FQDN. However one little piece that caused a problem was the "Add as Colleague" control on the profile. This by default when browsing via the "HTTPS" URL tries to access the internal URL in the following format:
So back to jQuery again, using the following I managed to modify this based on the protocol being "HTTPS".
The key was to attach to the class of the button, which is ".ms-my-addcolleague", grab the "onclick" attribute and override this similar to the code I used before. Once done the colleague button then worked for both internal and external access whether "HTTP" or "HTTPS".
JQuery saves the day again J