Some Achilles pain is considered "normal" while transitioning to barefoot/minimalist running, but it sounds like you may have actually damaged yours. Mine ached quite a bit now and then but it was never so painful I couldn't run.
I would suggest downloading and reading this free copy of Jason Robbillard's "The Barefoot Running Book" if you don't already have a copy. He is making this available himself so don't worry that it's an illegal download or anything.
http://www.mediafire.com/?mvlk66bp7i5lh7a
Good luck on a quick and full recovery!
Derek
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