Sigh. I was really hopeful this would work. I tried syncing after taking all of the steps you mentioned, first without doing a restore and then doing one, to no avail. Oh a few more photos did make it over, so I got to a couple of hundred out of 5200. But that's it.
I really think it's great everyone is taking the time and effort, to say nothing of patience, to work through attempts to resolve this. That's one of the real benefits of forums like this. But I am pretty much done with trying. Think of the hours you all have collectively spent trying to get this to work when it should....just....work! Resizing photos, restoring and resyncing, deleting files and folders, hours on phone calls with Apple reps who each have interestingly different takes on the problem. I find it especially ironic, but not surprising, that the "Geniuis Bar" is anything but. Historically I have known more than anyone I have talked to at an Apple Store.
Though of course they have not admitted any problem, Apple should have enough info to isolate the problem. Somewhere between iTunes, iOS 5.1, and the new iPad firmware lies the problem, especially when you consider syncing with all other "iDevices" continues to work fine. Very disappointing that a basic, but hugely significant, issue like this goes ignored and unresolved by Apple.