Greyed Out Tones and Music. Tones won't Sync.

Question

After restoring my new iPhone 6 from backup of an old iPhone 5 via USB, I added my tones and music to my phone.  I have manually manage music checked off.  When I checked my phone, I noticed that not all of the songs were there.  I preceded to download a few new alert tones that day. 
When I plugged my iPhone back into my computer and attempted to add the songs that weren't there, I noticed that a lot of the music that I had put on my phone was not showing as On My iPhone and that a bunch of greyed out songs with a grey circle icon next to them appeared as if the sync didn't finish.  I deleted the greyed out songs, added the songs that were missing and then synced.  The greyed out songs reappeared. 
In order to get rid of the greyed out songs, I tried a bunch of the tricks I've seen on the forums.  I unchecked manually manage music and resynced.  I even restored from a backup.  The grey songs still appear.  Now, the tones that a recently downloaded appear greyed out as well.  When I try to manually transfer them to my phone, they won't sync.  Anything previously purchased before the backup is able to be deleted and re-added with no issues. 
Any help would be greatly appreciated. 
Using iPhone 6 with iOS 8, Windows 7 Ultimate SP1 x64 with iTunes 11.4. 

Answer 1

I have the same problem now and had it in the past.  I had this on my 4s for more than a year. And hoped it would go away with a new phone.
Yesterday i bought my iphone 6, restored from backup. Was able to add a few songs (about 50) without issue. Then this morning i began adding about 6 gbs of songs and though it said it finished copying them I ended up with greyed out entries. I also got an error "56" something saying "can't sync."  I've also had this problem accompanied by my iphone not being able to show the proper embedded art. and i mean the art actually part of the file not just in a folder. It simply wasn't reading the file. It was reading an incorrect directory of artwork that was associated with the wrong song for some reason. But i digress.
I fundamentally think the problem is our backups are bad. I've read before that completely erasing the and reverting to factory settings fixes it. Personally, though painful i'm going to do that. I took a risk choosing not to do that yesterday. I think something is corrupt and all i've done, is copy bad settings to a new phone. Because, i haven't factory reset my phone since i first got the 4s.
In the past i read tons of threads. I've read possible causes are unplugging during sync but i haven't done that as i've had this phone one day. I've tried full reinstall of all itunes, multiple versions of itunes from 10, 11, 12 etc. The problem remains. I've fully removed EVERY ounce of itunes even the hidden files and it didn't fix the problem and eventually the problem reoccurs. In fact even when i've gotten it to sync the greyed files the problem eventually occurs.
Some things i've tried that have helped. 1, through itunes, delete some greyed songs. That once got it to wake up and it copied the grey songs. Again the problem did return. 2, delete all the music on the phone and copy it back. Always had the problem reoccur.
The one thing i've never tried is a factory reset because i didn't want to lose ios 6 or some podcasts that were on my phone but were no longer available for download so i didnt' want to lose them. Later tonight i'm going factory reset my six, and delete ALL backups on my phone or in icloud (not exactly sure how i do this but i'm doing it lol). Then i'm going to start completely fresh.
Oh FYI, I manually manage music. I don't sync anything. I drag and drop 100% of media, i don't let itunes manage folders either. i'm on windows 7 ultimate sp1 32bit on a PC. Oh and i've had this issue on multiple windows 7 machines, and multiple versions of itunes. On ios 6 and ios 7.