Personally I would hard reset the phone. I plan to do that after I get Black. It's a good way to start the phone fresh and get any bugs out. If you really want a fresh start just use NSU (Nokia Software Updater) it downloads and installs a fresh firmware.
If you use backup prior to your reset the phone will automatically start downloading your apps once you sign into your WP with your MS account.
For backup - Settings -> Backup -> On -> Backup now
You can even backup your SMS. However all game saved data will be lost. You'll need to backup Whatsapp data separately.
If you do decide to reset and you got everything setup and you find some contacts are missing, just create an Outlook.com email address using your MS account and you'll get the contacts.
Honestly, there's no other way around this.
You can try the storage option under Settings -> Phone Storage -> Swipe left -> delete Temp files. It may help.