I am not sure how the MFS comes into play here, unless there are children involved. You always have the choice to file MFS, but just watch for the itemized rule (if spouse itemized, you must also itemize).
Generally, filing a tax court petition does not get you to tax court. What you get is a very advanced auditor who will review the case and try to settle. I have had 4 of my clients file a tax court petition and none of them went to court. Everything settled out in the tax payer's favor every time. However, I did have rock solid documentation every time and the issue was that the the clients did not respond in time to other notices, and the tax amount due was really not in question.
I would definately preserve the ability to go to tax court by having the client file the petition. It is only a $60 fee and you preserve all of his rights.
But first, make sure that the tax return as filed is correct. This is the most important thing. The IRS cannot arbitrarily change his filing status, so if the return is correct and filed as MFS, this should be a no change review that will save him $1,100, minus the filing fee and your bill.
But something is bothering me about the facts as you have laid them out. I would look very carefully at the 2011 return. It doesn't sound right that the IRS only changed his filing status.
Good Luck.
Tom
Hollister, CA