Tony,
No problem, this stuff is confusing, probably more so with the meds.
The PEB is supposed to determine if you are fit to reasonably perform the duties of your office, grade, rank, or rating. This has been interpreted to mean your Primary MOS. It does not include details, or specialized duty (for example, in the Army, and infantryman is not unfit simply because he is assigned to an Airborne unit, but is unable to jump out of an airplane).
Your Commander's letter should address your limitations and how it impacts duty performance. However, any conclusions/recommendations about your ability to perform as a recruiter are not helpful. If he includes them, fine, but it is possibly irrelevant to your duties as a crew chief or mechanic on the flight line.
Yes, being incapacitated or missing work excessively are both reasons for unfitness. In your particular case, your limitations would likely apply to almost any MOS, so this may not be an issue. I state this in regard to migraines, but this may not be so for other conditions you may have.
Hope this cleared it up a bit. If not, I am happy to explain again in another way.