Woohoo! I now have a lovely new WM6 device. I not with some amusement that it tells you in the FAQ that you can't do the ROM upgrade with a Mac. Oh yes you can, thanks Parallels!
Anyway, upgraded Missing Sync to version 4.0 last night straight after the ROM upgrade and it connected immediately, in fact I think it's quicker connecting than before. Synced all my contacts and calendar back, reinstalled my regular apps and I'm good to go. The whole process from start to finish only took about 2 hours including the reinstalls.
Am liking the new version of the the Messaging App. Haven't noticed any key issues yet Gav, but I'm using Papyrus for my calendar.