This wait is of course made worse by the fact that NanoStudio just came out... Right now I'm a little scared - sync is going pretty fast, and iTunes is installing the missing apps (Unify-Zooloretto) ONLY. If it's doing what I think it's doing, I'm gonna have to start again with an older backup.
Well the sync did what I expected, I now have a stable iPod with all my photos and just a handful of apps. Here's hoping an earlier backup works... EDIT: Seems that there isn't a backup from when iOS4 did it's thing, previous backup is from May 5th?!?
Hrm, well it seems that the backup was good after all - however all of the apps up to that point in the alphabet (Uniwar) were unchecked (I don't sync all 2600+ apps in my library...) Going to the applications tab and checking apps (I did a subset of the important ones first) shows that my app data appears to be intact! So, I just need to put about 250 apps back on and I'll be in business! Next time I think I'll try the backup/download OS/restore method I've read about so much in the past few days. And major kudos to the developers of The Quest for enabling File Sharing so I can directly write that app's save games to my computer!