Hey all!
Is it possible to integrate Special Jobs (Holy Knight, Skyseer, Rune Knight), or even Guest and Enemy Jobs into the regular class tree, so you can level up and gain these classes for anyone to play?
No. It's maybe theoretically possible - but no.
You can't add new jobs to the wheel. What you can do is completely change some generic job skillsets, effectively replacing them. Simply adding their abilities to the generic job skillsets is also an option. However, I strongly recommend leaving specials' abilities where they are,
especially if you don't change swordskills to be evadable and with Mp costs. If simply moving them is all you want, with no other edits or balances, then it'd be best not to. Those abilities are meant to be limited to unique characters for a reason, they're very powerful. If you're determined to do so then this link will give you a good idea how to make these ability changes.
http://ffhacktics.com/smf/index.php?topic=11765.0
EDIT: The RAD spreadsheet can expand the job wheel to a degree if you want to take a crack at it.
http://ffhacktics.com/smf/index.php?topic=7031.0