So I've been keeping up with the monthly updates (not that anybody cares) and all is well. The current client version is still 3.5.1. I think 4.0 was where Blizzard essentially drew a line in the sand when it came to private servers. They've set the community back years in terms of content and in terms of the technical measures they are employing to break compatibility in every point release in the 4.x.x series.
Anyway - I just got a nice external SATA RAID 5 array that I moved all of the ManGoS databases and resources too. Everything on the private server runs so much better now that it is just amazing. I've had some fun playing for the last few days. Still trying to break into level 60 with my BE Pally. Oh well