1.3.3 might have helped not show books you didn't expect. At least the preview can tell you when things might double up. Difficult to track down issues with lots of customized templates, etc. - thanks for testing them out.
It does take a few seconds for Calibre to recognize connect/disconnect since its not checking every second. Makes debugging fun - which is why I allow it to run against a directory copy of the Kindle when testing at least some parts
1. You should get a warning if the Kindle is not detected, or if there is no metadata.calibre file already. It may be that you are running the plugin after disconnecting in a way or at a time I didn't check for. I'll need to retest all the scenarios, but if you remember what you did, let me know.
2. I'll check into the collections.json message. I made it an error in case there was a problem with the connection - but its much more likely that its a first time collection creation - and creating it if it isn't there isn't going to hurt anything.
Great stuff - thanks again for all the help and encouragement