ad 1+2) No, the limits on the website only apply to the cloud-hosted version. When you host it on your own, there are no limits with regards to storage sizes or message counts.
ad 3) Recent Mattermost versions come bundled with the Boards plugin (Focalboard deployment) so all you have to do is activate the plugin and it will seamlessly integrate into your Mattermost experience.
If you already have an existing focalboard server, there’s unfortunately no way to connect the Mattermost plugin with the external server, but you can export the data from your current focalboard setup and import it into Mattermost Boards.