1. Can you create extra fields (custom fields) when a file is uploaded to store extra details on the file, like a comment box in addition to the description.
No, they already include a description where you'd put your comment. CB Gallery can have commenting using CB Activity and CB Auto Actions though. GJ can not have commenting.
2. If you upload to group jive, can you stop everyone seeing your uploaded file apart from the owner of the group. I know the purpose is to share information but I am trying to use it for a specific purpose.
Only if approval is enabled then it'll be pending approval and only visible to the group owner, group moderators, group administrators, cb moderators, and the owner of the file.