My iMac apps are not linking to relevant files in ICloud

Question

IMac applications not linking to relevant iCloud files
My iMac and relevant software apps will not link to my files and documents in iCloud. This includes Apple apps i.e. pages, numbers etc and 3rd party app i.e. pixelmator etc.
Also back to my mac will not work getting a "iCloud server not responding" message every time I deselect and then try to reselect.
The iMac is linked to my apple ID and shows the files are there against each relevant app listed in the 'manage' pane for the iCloud system preferences.
All the files show on my iPad and can be opened there.
If I save a file eg a page document to iCloud it just show waiting even after hours. It's still on my hard drive, but does not upload.
My mail and calendars are fine and linked to iCloud & iPad etc
I have tried
1/ repairing permissions
2/ checking key chain
3/ reinstalling the apps
4/ reinstalling OSX ML
5/ formatting the hard drive and reinstalling OSX ML
6/ logging out of my account and relinking many times
7/ said prayers etc . .
I have all ML updates that are available

Answer 1

Try booting into the Safe Mode.  Disconnect all peripherals except those needed for the test. Shut down the computer and then power it back up. Immediately after hearing the startup chime, hold down the shift key and continue to hold it until the gray Apple icon and a progress bar appear. The boot up is significantly slower than normal. This will reset some caches, forces a directory check, and disables all startup and login items, among other things. When you reboot normally, the initial reboot may be slower than normal. If the system operates normally, there may be 3rd party applications which are causing a problem. Try deleting/disabling the third party applications after a restart by using the application uninstaller. For each disable/delete, you will need to restart if you don't do them all at once.
Safe Mode
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