@karljian
Whatever instructions you find, keep a couple of things in mind.
(a) You are no longer starting from the beginning. There have been a few actions taken, by you, your spouse, and the IRS, that complicate the situation. I don't think you are going to find any instructions for what to do at this point.
(b) Your wife's options may be limited by the fact that it is now after the due date of the return. You cannot change from MFJ to MFS after the due date of the return.
Also, in your original question you said that the IRS letter asks for "verification such as divorce decree." That doesn't make sense. You would not need a divorce decree to file as married filing separately. In fact, a divorce (before the end of the tax year) would prevent filing as MFS. So there must be some kind of mistake or misunderstanding somewhere in the chain of events.
All these complications are why I think you need to get a tax professional to straighten out the mess that you are now in. This is no longer a do-it-yourself project.
