I think the option you want is “Restore missing apps with data,” but you are right – you have to go through that list and uncheck the system apps. Clock widget 1.00 has probably been replaced with a more recent version, so I wouldn’t restore that.

I’d make a nandroid backup as a 2.2 “stock” rom, then restore all your apps that you know you downloaded and installed. Make another nandroid backup as a “stock + user apps” You should be in good shape after that.