I have just created a new extension that makes joinTime an editable attribute via the REST API. There are no controls in the frontend for it though. I have not yet tagged a first release so only version :dev-main can be installed at the moment https://github.com/clarkwinkelmann/flarum-ext-editable-user-attributes
Author Change extension can be used to change the date of existing posts and discussions.
I'm not sure what you mean by that? The missing IDs are probably users that have been deleted. If you are referring to users you did not create, maybe those are bots or users who discovered your website?