My advice is to consult a local tax professional or tax lawyer who has experience representing clients before the IRS. You are allowed to change from MFJ to MFS before the due date of the original tax return, but doing so is very rare. I can't find any IRS instructions for how to do it. You are not likely to find a tax professional who has ever done this for a client. The Internal Revenue Manual, which is a manual of procedures followed by IRS employees, says that you can do it, but it doesn't have any instructions for the taxpayers. You can tell the tax professional to refer to IRM 21.6.1.5.5.
When you meet with the tax professional, bring copies of your original joint tax return, the amended returns that you filed, and the letter from the IRS.
