Hello MattF
A bit hard to read your questions here. Perhaps it would be easier for us to help you out if you include us in your intention with your solution. Right now you're narrowing it down a bit too much for me to give a good answer :)
But ok - if I understand your nr 1 question correctly you have a clearpass that hosts multiple sites. If I register on Site 1, and then arrive on Site 2 later that day, I get treated like it's the first time on that ClearPass.
How are you treating or categorising/enforcing your "returning users" today? Knowing that can lead us closer to a solution.
It really shouldn't be that hard to implement, but it might cause some user-issues..
Username need to be different, so add in prefix+random-number as username.
If you're doing MAC-auth, that too will be solved by site-unique usernames..
For question 2 - depends on what you want to accomplish ;)