What does your profile say? Do you have a profile for the headache effects? for the arm and leg weakness? That will be the major driving factor for the MEB. If the profile doesn't address the issue, most likely the MEB and NARSUM will say they meet retention standard. Make sure the commander's functional statement addresses these issues. If the commander says they effect fitness, the PEB should take that in account despite the MEB. I am assuming they are MEBing based on the stroke, and for you to fail retention standards, they have to identify which residuals are causing the problem.
The VA when they rate you on the stroke are supposed to base it off the residuals. The current work order as I understand it is the PEB finds you fit or unfit, that way they find you fit overall, the whole process can stop. Then the VA rates all the different conditions. Then the PEB takes those conditions the VA rated and say which ones are actually unfitting. The NARSUM may just say the stroke or whatever is the referred condition, but as long as they break down why in the written portion, it should be ok. They can say the stroke is what is causing the unfittness, but only the leg problem, and hence the leg rating, is unfitting and say the arm and headaches are fine. Just make sure information showing the others are effecting you ability to be a Soldier gets to them.