You can amend from separate to joint at any time, there is no deadline. However, refunds will only be paid if the amended return is filed within three years of the original deadline. So, unless there is some other strategic reason to re-file your 2011 return as MFS, it may not be worth doing.
You would file one amended return converting one MFS return to MFJ. That will automatically cancel the other MFS return. However, TurboTax 2011 is no longer supported, so you may need to see a tax professional or do the paperwork by hand using the 2011 forms download it from the IRS website.