I will try to answer your questions in the order you submitted them.
1.) Yes, it is best to use the CD version.
2.) Yes, your home state is Michigan. By filing New York first you will have the taxes paid in NY to get the credit when you post Michigan. However, If 100% of your income was in MI, and 100% of your wife's was in NY it will not make a difference, (Your wife may have to file part year resident in both MI and NY using NY).
3.) Yes, you will have to create two mock Federal returns, each showing your individual income. One for you and one for your spouse.
4.) Your Mock return will print with the filing packet.
If you have TurboTax Live you certainly can call and have an expert walk you through.
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