Yes, she would only be exempt for 5 years maxium as well therefore she is now a resident for tax purposes.
Yes you can apply for ITIN and file married filing jointly. Please see How do I apply for an ITIN?
Yes, you can use TurboTax to file an amended return (1040X). Please see FAQ How to amend a tax return for instructions on how to file 1040X.
Please see the links below when Form 1040X is available:
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