I'd suggest you try restoring from backup when you were done. I've restored from JB backups plenty of times on my 3G, 3GS, and 4. And never had any problems with it.
Please next time search, this has been answered multiple times. Your methods are correct so you can try either one, the upgrade over the JB would be the best method since you wont need to restore from backup. At the worste you may need to put your phone in DFU mode if you get errors or the phone wont reboot. I have never had any problems, so just make sure you backup and sync before starting either method. I also restore from backup ALL the time too, I wish people would stop saying not to and instead say to restore as new if there are problems.