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After you file
You have to wait for her return to be processed and then amend hers to change it to a joint return. If you try to submit a joint return right now, it will just be rejected because she has already filed and her SSN has been used. Wait until her return has been fully processed, and the refund has come in. THEN prepare a 1040X for her return and make it a joint return will ALL of your income etc. on it.
A 1040X cannot be e-filed. It must be printed and mailed. It will take about 3-4 months for the IRS to process an amended return. It is a good idea to use a mailing service that will track it, like UPS or certified mail, so you will know it was received.
Wait about 3 weeks from mailing and you can check the status of your amended return:
https://www.irs.gov/Filing/Individuals/Amended-Returns-(Form-1040-X)/Wheres-My-Amended-Return-1
https://ttlc.intuit.com/questions/1908543-do-i-need-to-amend
https://ttlc.intuit.com/questions/2566895-what-does-it-mean-to-amend-a-return