Hi Erica -
Thanks to Nancy for sharing the sharepost about ADA, which might help if there are ways to make your work environment better or accommodate your Migraines at work. Is there any way you could arrange some flex-time, tele-commuting, or other options that would let you get the work done around your migraines? These are sometimes accommodations that people have arranged under ADA. You might also want to read about Using FMLA and ADA together - just because you are using FMLA time does not let your employer off the hook from accommodating you!
To qualify for SSDI you need to have first been totally disabled for 6 months. Here's some information about Social Security disability in another question answer that might be helpful. Unfortunately it's hard for a lot of us who may be in that gray area between totally disabled and just missing some time due to migraines.
Good luck!
- Megan