I'm not the op but I always have trouble with updates, restores, and syncing. So maybe by answering my specifics you will help the op as well.
Whenever I need to update or restore my iPhone it always seems like a pain in the butt and takes hours. Let's use the example of when I got my 4. First I transferred purchases and backed up. I then plugged the new phone in, set it up and restored from backup. When this was done things like my settings, wallpaper and contacts were back but none of my apps. I then went to the app section, clicked on sync apps, checked the ones I wanted and hit sync. Well THEN when I looked at the phone none of the apps were in the right place so I then hit restore from backup AGAIN and "most" of them were back where they belonged and in the correct folders but none of my music was there. So I had to go to iTunes and put all my music back on (all 1400 songs). I've read people saying just sync your music and it will go back however I can't do that. First of all I have too many songs to fit and I have music in iTunes for 5 people. I really don't want my little sisters Justin Bieber and I don' think she wants my sons metal or rap. This was all very time consuming.
These are not the only problems I've had. For instance when I go to update I transfer purchases and backup then update. I've read where people recommend to set up as a new iPhone/iPod however whenever I do that as soon as it's done it backsup again, thereby making that the most recent backup. I then have to go to the location where it stores the backups (which requires me to google to remember where that location is and showing the hidden files) and delete the most recent one. Then go back and restore from backup, sync apps, and restore again. Still no music!
We recently got my sisters new iPod touches and in trying to restore them from there old 1 gen had all these same problems. It took HOURS!
I just know there has got to be a better way to do this. Plus I'm concerned because now my phone is jailbroken and I have ALOT of specialized settings. What am I going to do next time