I've been having the same problem. It would either get stuck at "Waiting for changes to be applied" or "Waiting for items to copy". My last successful sync was on 10/15. Tried a number of times either via wifi or direct connect.
Solved it in the following fashion:
- Connected the phone to the computer via Lightning cable.
- My phone was set to back-up to iCloud. Changed that setting to back up to the computer.
- Unchecked the "Sync Music" option under the music tab.
- Hit apply.
- After a wait - the back-up completed and all the music was removed from my phone.
- Once it was done, re-checked "Sync Music" - it got past "Waiting for Changes to be Applied" at this point.