Ok. Thank you so much for your detail response. Let me break down the different laws in place here.
You've worked there long enough and often enough for the FMLA to apply. Now, that being said, the FMLA only applies to employers that have at least 50 employees within 75 miles. I don't know how many locations you have near you, but hopefully there are enough that it would count as a large enough employee. I don't know the business situation of Little Caesers though...are they just franchises or are they centrally owed? If they are franchises, does one person own the multiple locations in your town?
Because the issue here is that for the FMLA to apply, you have to aggregate the employees in different locations to get to the 50 within 75 miles and they have to be with the same employer. If different individuals or entities own the different franchises, the FMLA doesn't apply and that may be why you were never asked to apply for it. The FMLA would protect you from discipline for your absences, as they would be approved under the FMLA, up to 12 weeks in a year. You need to explore this, even considering filing a Department of Labor complaint to determine if the FMLA is applicable. If it is, then you should have been offered intermittent leave to cover these absences that you have had due to the migraines, which can qualify as a serious health condition under the FMLA.
The next issue then would be that this is disability discrimination. Now, the problem is that if you can't really work, there is no accommodation the employer could give you to allow you to work. So, I don't see a very strong ADA claim here. It seems that they gave you some time to work the issue out, but if you can't work in your condition in the food industry, they don't have to create a different job that you can work in. Unless you can come up with a reasonable accommodation in your current job that would allow you to work with your disability, there isn't an EEOC complaint that you could make.
That would limit you then to the Department of Labor claim, if we can get FMLA to apply here. I think it is worth your time and effort to file that claim. It's free and you can't legally be retaliated against for filing it. Sometimes, just filing it is enough to get a better resolution from the employer.