How do I file MFS when the wife has no SSN or ITIN in proseries tax?  The system will not allow me to put NRA as it gives me an error message that its invalid.

If I remember correctly, you need to ignore the error message and file by mail.

MAYBE you could disable error-checking when e-filing, but I suspect it would be rejected by the IRS.  But it may be worth a try before filing by mail.