A 3-Month Wait since my IRS Filing was Accepted

Dear TurboTax:

I have used you guys for more than 10 years and love your service. However, never before have I experienced such a prolonged wait for my refund: literally 3 months now and counting since my Federal Return was Accepted by the IRS. In March I received a letter from the IRS with a Control Number and Letter Number. I responded with the identiy information they requested and was then congratulated that my identity had indeed been verified. After several more weeks of checking its status to no avail, I contacted your TaxAudit partner and although they were helpful and responsive, the could tell me nothing further. I have never in my adult life experienced this kind of delay in obtaining my refund. And this year I filed in late January! In fact, my California tax return was filed then and I was granted my refund in 6 days. 

What in the world is going on and where can I turn to now?

Lance