Our AD server is cloud based. As above when I attempted to run this on the MoodleRooms sandbox and my own private development sandbox we were completing this synchronization in under 15 minutes. Given the discrepancy between that and the reliable 5 hour run time on our production in MoodleRooms I'm out of ideas as to what is causing the disparity in times.
I'll follow up with MR and see if they'll try adding the microtime() to measure what's going on.