>>I hope that summary is more clear<<
I do not think it is clear. Maybe it makes more sense with the documents in front of you, because for one thing, I can't tell what 1099s were issued, when, or for what tax year. For another thing, I am confused by the original 2011 return referring to an undocumented rollover, and then responding to a CP2000 with a 1040X apparently restating the same position. I can't tell when or even if an RMD was really made. Frankly, I'm still not convinced that the IRA was actually maintained as an inherited IRA rather than being distributed in full. I'm not even convinced that's what the client intended to do. So I have to say that at this point the notice of deficiency sounds correct to me, at least in terms of failing to respond to the 30-day letter.
Now I suggest you write out a timeline. Each step should have a date and a complete sentence, but the sentence should have no more than five or six words. Somebody sending something and somebody receiving the same thing are two separate steps. Stack all the documents in chrono order and mark each as Exhibit A, B, C, etc., and add a reference on each step. Those documents should include everything relevant--not just the 1099s and tax returns, but your organizer or interview notes, whatever the client signed at the credit union, the IRS letters and your replies, your telephone notes with client and IRS. You don't need to copy this thread, but you should consider the trust, will, and/or beneficiary statement.
Meanwhile I think you should explain to the client about petitioning Tax Court (do some quick research first!) Trust me, the court will send this down to Appeals, but it might be the only way if AUR gives you idle promises or refuses outright to talk any more. Also discuss your client's other options, including just paying the deficiency in full or installments. (Presumably you can still get the penalty waived.) After all, it's going to be due in a couple of years anyway. Even if you win in the end, fighting the IRS is a big drag on the psyche.
Oh, and don't forget the state return.