The greyed out tracks and dotted circle icons would seem to indicate that iTunes has stalled during a transfer and now isn't properly accounting for what is and is not already on the device. Sadly it doesn't recover gracefully from this issue.
You could try the following all-purpose steps for dealing with erratic device or sync behaviour. They assume that all of the content you want on the device is in your library ready for restoring. If it isn't see Recover your iTunes library from your iPod or iOS device first. I would also recommend you copy everything out of the camera roll if you haven't already.
- Backup device.
- Restore as a new device.
- Restore the backup you made earlier.
Use an encrypted backup if you want to preserve passwords, Wi-Fi settings, web history and health data where appropriate. I also suggest syncing with a selection of playlists (unless you're using iCloud Music Library) rather than manually adding content as, if nothing else, the process above is easier to do if you ever have to go through it again.
It is possible that using Settings > General > Storage & iCloud Usage > Manage Storage > Music > Edit > All Songs > Delete on the device and then resyncing will produce the same results, though it may depend on exactly why things have gone wrong in the first place, and it might not help with Tones anyway
tt2