1. Yes, you can use the SSN she was issued when working at Disney. The SSN is forever and does not expire.
2. That will depend on your situation. Every situation is different. Her income prior to getting married would be taxable by the US if she filed as a full year resident and only partially taxable as a Dual Status Alien. For some people it makes absolutely no difference if they file joint or separate. Generally, the biggest difference is the standard deduction is $13,850 if separte and $27,700 if married filing jointly. If she has income, then the difference in the standard deduction may be offset by her income and not cause you to see a benefit. The are some credits you may not be eligible for, such as education credits if you file separately.
Married Filing Joint versus Separate
3. You would enter your wifes income in the foreign income section of TurboTax by selecting Income>>Foreign Earned Income and Exclusion under Less Common income. This will allow you to not only enter her income but also take a credit for taxes paid to Japan.
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