Pharos recently released a Hot Fix that addresses using the Pharos Print Center with Safari 9. it can be found at the link below.
And there you go...not sure why I didn't check there first!
After installing the update, however. My Safari 9 clients are still not able to authenticate. I have verified that we're on the right versions for both the API and PrintCenter and have restarted IIS a few times with no change. I can't restart all services now but perhaps that will fix it (even though I don't know why it would).
EDIT: Got a chance to restart those services and sure enough, Print Center seems to be working now.
Thanks Jason and Jeff. I had to apply the Hot Fix to correct the issue with Safari 9 not able to authenticate through Print Center. I restarted my Uniprint VM and had to restart IIS to get the changes to stick.