iCloud not syncing and Contact problems with merging duplicates

I was having problems with the syncing of my notes app. When I got the iphone 5 I had since using Mountain Lion I had started to make use of the fact that the notes sync across iCloud. Great. Although not for long. Everything was going fine notes were syncing across devices but then spontaneously they stopped syncing for no apparent reason. I then went to look in settings, looked online and all through discussion forums. Switching notes on and off on icloud both on the macbook and on my iphone. Restarting devices etc etc. iCloud itself online was not able to access the notes app. I kept getting error messages that I would submit to apple. Then I finally relqinquished and unhooked the iCloud accounts from the computer and phone. And at the sacrifice of losing albums in my photostream they sprung back to syncing.

Then the real problem happened. I had selected to keep a copy of my address book in contacts when I unhooked my computer just in case. When everything linked back up again, I then had duplicates in my address book. Not 1 (this can happen just having icloud active) but 5 sets of duplicates, granted I had kept a version from when I unhooked. So I looked around again for how I could quickly and easily get rid of duplicates. Following suggestions online I go into contacts>cards>look for duplicates. I had 1200 or somthing duplicates, so naturally when given the option "would you like to merge the info in these duplicates I click yes. The MacBook starts to chugg away. Its gonna take a while. So I come back later. And before returning to CONTACTS, go to send a message from MESSAGES and I notice that 80% of the threads have no name. I go back to CONTACTS and WHAM 100s of contacts disappeared in the merge never to be retrieived again. You cant restore CONTACTS from Time Machine as it is just mirrors the contacts that you have in present time. Restoring phone doesn't work becasue it just downloads from iCloud after it has restored. TOTALLY RIDICULOUS. I am livid.