Then when an anonymous lead becomes known (fills out a form) we populate a custom field to designate which of these sources was the first, original source.
We were leveraging Google Analytics referral URL tracking as part of our solution and recently upgraded to their most current tracking code (Universal Analytics). Our JS no longer works with this new GA code so I'm wondering if any other customers are tracking anonymous leads this way AND using Google's latest Univeral Analytics code.
You would have to provide a URL so we can see where your code is breaking.
In general, it's not a good idea to couple a separate attribution tracking script closely with GA, since GA is definitely not intended to be a client-side API for other scripts. GA doesn't have any special access to session info that decoupled, dedicated code can't get on its own.