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You can contact the IRS and request transcripts (phone, letter, problem resolution office, through your CPA or other tax professional with power of attorney). If you are due a refund, but the IRS hasn't or won't issue you one, despite all the necessary paper-work having been filed, you'll have to send a notice/explanation/proof to the IRS in order to get the refund. Normally, filing a return and/or a refund request will trigger the refund, but your situation is past that having already filed, received a refund, paid money, etc. etc.
This really sounds like something you should get some professional help for, if you haven't yet.
The FTB is the "Franchise Tax Board."
Any amounts they've taken have gone to CA and not the IRS. You would essentially go through the same process of figuring out where the money was applied (what tax form and year). After that you'll be able to get to the bottom of the situation.