According to that debug log, calibre found 144 books on your device and did not produce the exception described in post 3.
Code:
DEBUG: 19.9 USBMS: count found in cache: 0, count of files in metadata: 144, need_sync: True
You should see these books in calibre's device view. Do you?
Note that the "Failed to read MOBI cover" is not a fatal error, probably caused by the books being infested with Amazon's DRM (Digital Rights Management).