Should I list this condition on applications?
For some positions, applications ask many questions about the physical ability to perform a job. That isn't usually the case for software engineering in the US, but I have still seen it happen.
Some of these applications ask a final question along the lines of "Do you have any limitations that could prevent you from fulfilling this position?" In that case, you need to decide if your "days that will affect your work performance" should be disclosed or not.
If the application doesn't ask these sorts of questions, or if you feel that your condition would not be a limitation, then I wouldn't expect you to disclose it on the application.
If not, when (if at all) during the interview process should I tell
If you will be asking the company for special accommodations for your condition, then you must discuss them before accepting an offer.
I would wait until you sense that they are very interested, and about to make you an offer. During your interviews, try to sense the culture of the company, and in your own mind if this is the kind of environment in which your background would or wouldn't be an issue.
Remember, you want to find a great fit for yourself - one in which you can excel. You want an employer who can work with you to deal with your condition and still be successful in your career, not one who will quickly be looking to marginalize you, or looking for an excuse to terminate you. You can only get there by discussing your situation before being hired.
If you aren't asking for any accommodations, you might need to consider if you will need to incur periodic absences (for ongoing treatment, for those 2 days per month, etc). As a hiring manager, that is something I'd want to know ahead of time. In many companies, it wouldn't harm your chances for the job, but in some it would. That's something you would want to know before agreeing to an offer.
And if your condition will neither require special accommodations, not incur periodic absences, not display obvious symptoms, then you may not need to disclose your condition at all. You may have things well under control, and thus there is no need to worry a prospective employer unnecessarily.
There are brain injury support organizations who can help you. You should connect with them and discuss the job search you are embarking on. They have much more experience with this than anyone here would.