I have been seperated from my wife for 3 years, i never knew her SSN or where she is to contact her. How do I file?

To file separately without the spouse's social security number you need to file by mail.  The return will not e-file.  Include a cover letter with the return explaining why the SSN for the spouse is missing.

If you can't find it, you will have to have to leave it blank, and see if it will let you print your return and file by mail.  You can write "refused" in the place for the SSN, and attach a written statement describing the situation (you are separated but still married, she refused, etc) and giving as much contact info for her as you can (name, address, phone number).