Update —
So I discovered that the problem wasn’t within the migration/files/plugin, but rather was a host related problem. I want to update this so that anyone who might have a similar problem might find this and not have to rack their brain nearly as bad as I did!
The problem ended up being that 1and1 auto-banned my IP when I tried logging into wp-admin and thus I lost connection and couldn’t reconnect. Made me think the server failed. A simple phone call to support (ok, not so simple since I couldn’t understand the support rep) and it was fixed. After he did whatever the links took me to a 404 page, and I just ran the rewrite permalink option and everything was back to normal.
I hope this can help anyone who is having the same problem.