Erratic syncing on iPhone 5s with iTunes 11

Question

I am going crazy trying to sync my iPhone 5s with iTunes 11.1.3.8. There is plenty of space as my iPhone is 64gb with apparantly 36.5gb available. Approx. 15.4gb of this is currently taken up by music, but it should be far more. I don't know if it is an iTunes problem or an iPhone problem - or both!
I've always added music to my iPhone manually by dragging folders on to the device in iTunes (with "manually manage music" ticked in the settings). This never used to cause any problems, and I prefer it to having all my music choices in iTunes as I have different devices with different capacity etc.
Since using my new iPhone, syncing is going wrong every time in strange and unpredictable ways:
1. Not all the music will sync, seemingly at random.
Some albums have the grey circle next to them and won't add whether I delete and re-add or not
Some albums had the grey circle but synced when I deleted and re-added (these are the same type of files and from the same source as the ones that still don't sync)
Some music suddenly shows up with the ! symbol and won't sync, for no reason - sometimes this is even a random selection of tracks on the same album stored in the same location.
Some music appears in iTunes as though it is on the device, but doesn't show in the iPhone e.g. out of dozens of Bowie songs only 2 show up on the phone
The last time I synced I added an audiobook of short stories, with each story as a track. When I went to listen to it this morning, around two thirds of the tracks had randomly disappeared. After syncing they seem to be back, but I have no idea why they vanished last time and if it will happen again.
Sometimes after syncing a whole playlist will have gone blank in the iPhone i.e. tracks aren't there, but when I connect to iTunes the playlist appears as it should be. Syncing sometimes fixes this, but might then empty another playlist...
2. I manually set compilation albums to "sort by album artist" e.g. changing my short stories audiobook to show under Artists as "Short Stories" rather than each author as an album with 1 track. At random, when I am looking through artists on my iPhone I notice that one or two albums have ungrouped, even though I didn't touch any settings in between.
3. When I'm connected to iTunes the usage bar at the bottom seems to fluctuate randomly sometimes. Currently, having just synced, it shows 15.4gb audio with 36.44gb free. Ok now I added 1 album which is 92.5mb and synced - just that one chance.. Usage bar now reads 21.76gb audio with 30.08gb free. Now I'm adding a 173mb folder of 2 albums and syncing. Usage bar now reads 15.51gb with 36.16gb free. Somehow after adding 3 albums and not changing anything else, I end up with more space than before??
I'm at a loss as to why iTunes/my iPhone is behaving so erratically. Perhaps the above are seperate, unrelated problems, but I'm writing them all here in case they are all linked to one problem.
I have tried syncing using the original cable and over wifi. Have also rebooted the phone and restarted, to no avail.
Please help me with some suggestions of what is going on and how to fix it? Let me know if you need any more info.

Answer 1

Hit there tayls22,
It sounds as if you are having some issues with your ability to create a backup in iTunes of your iPhone, which prevents you from completing the sync process. I have an article for you that can help you troubleshoot this issue further, and it can be found below:
If you can't back up or restore your iPhone, iPad, or iPod using iTunes - Apple Support
http://support.apple.com/en-us/HT203271
Thanks for using the Apple Support Communities. Have a good one!
-Braden