Where are you being asked for 2 forms of her ID? When you file the return, you should only be asked for your drivers license at the end right before you transmit the return. You should not be asked for anything at all other than her SSN and name and a couple other questions about her living with you and if she is claiming itemized deductions.
Are you sure you chose Married filing separately? Go back to the personal info section and double check.
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