I think I'd distinguish between headaches causing temporary recall and clarity issues vs. LDs that are always present. If he learns well (and it sounds like he does!) I'd call it a health impairment that limits performance rather than an LD.

It seems reasonable to me, if he needs standardized testing, to ask for accommodations (such as rescheduling if he has a migraine, or breaking it into smaller segments if he is in pain).

DeeDee