Syncing is just not working with Apps

I have 145 apps. When I sync, they are placed maybe one per page... total of 11 pages. (this in Itunes 10.1). I have upgraded to OS4.2. The last 3 pages in Itunes are gray, so those do NOT appear in the Iphone. I have done the restriction thing, it was never on restriction). Some ARE coming over. I have spent 2 days on this. I moved all my IPA files out of the folder to another, uninstalled Itunes.
Reinstalled it (even after this, all the apps were still in the list on the left side of the apps page (list of apps, picture of the iphone, list of iphone screens). There must be some file I didn't move or delete. I moved the ipa files back to the right mobile applications directory, then sync. all fubar again. I have reset the phone several times to factory settings. turned it off, closed Itunes, etc. at my wits end.
Music, photos all works ok in a resync.

I downloaded Safari 7.03 from an Apple UK site and reinstalled same problems.
The only way to  reinstall Safari on a Mac running v10.9 Mavericks is to restore OS X using
OS X Recovery
Exactly how slow is the connection?
Check your download speed here > Speedtest.net by Ookla - The Global Broadband Speed Test

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