For some reason some of the puzzles reset and now I'm stuck behind the first barrier with the wizards skull and can't access the surface at all now
Huh. That's weird! No idea what's up with that. If you'd like to go back through the intro/tutorial bit again, open up the game's files (should be in local appdata, look for "Transmute Deluxe"), go into the Options.ini file (you can open it up with notepad or a text editor), and look for the Respawn option. Then, set the x value to 1408, and the y value to 384. If you save that, and then reopen the game, you should start back at the very beginning (but with no forms lost) so you can re-open the puzzles as necessary. Hope this helps a bit!