With regard to the sync erroring out on calendar, take a look though the calendar on the computer. If you can change the view to rows and columns like a spreadsheet, all the better. Look for oddball characters, empty rows, and so forth. Clean up as needed. Also look at notes in calendar entries, particularly any that are relatively large in size. After you've cleaned it up, try to sync again. If you still have trouble, use advanced backup/restore to clear the calendar database on the device and then re-sync. Hopefully it works.
As far as dupications and that sort of thing, I don't know, except set desktop manager to ask for confirmation, and re-sync when it asks to make what you think are too many deletions, additions, or changes.