Chris, I am not up to speed with the resiliancy package, but from how I have seen it work it could be a pain, so I can't help you much there. As for the syching to get the names right, it is normal to for it to be done a couple times.
For example, if you have two switches A and B. When a sync happens opsman goes to pbx A and looks for changes, if it finds one it updates its directory and then moves on the PBX B. It propagates the change for PBX so that B is updated, but it may also find a change in B that has to go to A. It records the change, but will not go to deliver that change until the next sync, because it already looked at both switches. That's just the way it works, kinda a dumb.
As for YA 3, we have not installed any yet, but will be soon. We like the new structure as it is a better way of keeping track of how many are out there. The big drawbacks are for us is the fact hat you require a server now, which sucks for upgrades. Also if the server goes down your clients no longer work.
Simon