and when I restart into the remote disc form, I can no longer use the Disc Utility to check the MacHD
I have no idea what this sentence means, or what it could possibly have to do with Messages.
Why not just re-add your phone numbers and/or email addresses to Messages?
For the record, I haven't had to do that with mine, but I have noticed notifications when I would update the iOS or OS X machines that notified me that my usual emails/numbers were now being used by the freshly-upgraded machine, so there's obviously some kind of re-registration process used by Messages and FaceTime.
I use Messages nearly constantly now, either the Handoff function that allows me to send SMS messages or receive/make phone calls, as well as in a collaborative environment with work, and iMessages to friends with iPhones/iPads/Macs. Apart from a disappointing dropping of AOL chat room compatibility, Messages has been working as expected through the beta process and now.