Thanks for the follow-up questions, Emma. Here are my response in order:
Yes.
When I turn editing on, and then click the cog icon to edit a course activity I get taken to a page with this message, "Can not read file, either file does not exist or there are permission problems".
The Moodle 2.6 theme is entirely missing in 2.8. I had copied over the Serenity theme, which is what I am currently using in 2.6. The only themes available in 2.8 are Clean and More, even though base, bootstrapbase, canvas, clean, more, and serenity are folders listed under the theme folder. I have cleared the Theme Cache, but to no avail.
I copied moodle/* and moodledata/* to the new environment. I have tried this migration on multiple shared hosting servers, but they all result in broken links.