The whole "get a tax professional" posts are good advice, but I will just say that a very similar situation happened to me, and I DID NOT turn it over to our accountant, but DIY'd through it. They are not auditing you, they are "correcting" your money owed.
It sounds A LOT like you have your "ducks in a row." IF you decide to go "DIY", I would call them, explain the situation with the person you talk to, ask where EXACTLY to send a certified letter, by NAME, send a letter explaining the screw-up, what you did to correct it, and if your correction was timely, request that the penalty (if any) be waived on the basis of your employer messing up your original W-2. I would only go this route if your correction was done in a timely fashion and you have full documentation (as it sounds like you do).
I wouldn't be especially alarmed about the huge discrepancy between what they think you owe and what you think you owe. My experience was precisely the same, and I was treated perfectly reasonably. They waived my penalty and I was never audited. It sounds like the worst case scenario in this instance as you have described it would be a penalty on the 1100, and my bet is that due to the nature of the reason the taxes were underpaid...you are gonna get a waiver. If the local office is nearby, I think (if it were me) I WOULD take my paperwork in person to them. Call and see if you can get an appointment.
You are a W-2er, and this should not be so especially complicated...I'd call it pretty straightforward. My experience is that the human beings are a lot less nasty than the letters they generate, if that makes you feel any better. Based on your description of the situation, I'd lay even money that you are a 20 minute phone conversation from having this resolved. They will re-do the math on your amended return (once the human on the other end finds it in their computer) and declare you owe squat. They WILL send a letter to that effect, but I'd make sure to request it. A prediction.