Ken,
You don’t necessarily have to use media manager to copy the files. You can just do this at the finder level.
The 4 x 3 versus 16 x 9 issue is a settings thing. Somewhere along the line you’ve lost the correct settings on your media. This is another reason why NOT to use media manager and just copy the files.
I think your media manager settings have screwed up the passing of media back and forth. It appears that you have created “independent clips” with the incorrect setting.
Try taking just the media, moving at the finder level and then see what happens.
Good luck with your “avid vet”. That’s your problem… not ours. 🙂
Mark