In your case I'd say the macro errors you're seeing are probably the culprit to your problem. In every upgrade after I have successfully upgraded the code and database, after I'm able to log in, I check the event log and fix any major issues then I resign all the macros. I've had it where full sections of the Kentico Admin UI were not available because of macro signatures.
If you're not able to re-run the upgrade then I'm afraid the way to stage the items is make a simple change like you're mentioning. Another way is to run an export of the global objects from the Sites app and uncheck everything, then go back and check items in which you want to export and import them into your live site.