Hi, Saundra. My daughter had two indirect bypass surgeries in March, too. Before then, she had two strokes (in January), which finally led to her Moyamoya diagnosis.
Daphne had a history of seizures before the strokes. If Nathan had an EEG done yesterday, you should call his doctor. EEG results should be back by now, and they should give you an idea if Nathan has the potential for seizures, or if the jerks might be something else.
There are some seizure medicines that aren't good in moyamoya, but there are others that should not cause a problem. As Cara'sMom mentioned, Trileptal is pretty safe.... there are others, too. You just want to be careful of something like Phenobarbital that can lower blood pressure. My daughter has been on Vigabatrin - which is not FDA approved - and has not had any problems with it.
I agree with DJ's advice that Nathan should get an angiogram. An MRI doesn't really tell you all that much about blood flow, unfortunately

I also agree that if Nathan's doctor is not sure about the next step, or what seizure medicines to try, you might consider traveling to see Dr. Scott or Dr. Steinberg (in California). They are true experts in the field, and can probably steer you in the right direction. Even if you aren't sure that you can see them, you can still send your son's studies and surgery report to them and get their opinion.
We were told that it takes three to six months for the blood vessels to grow in (and they continue to improve after that). I do think that six months after surgery, Nathan should have a much less risk of stroke -- so I think you are right to be concerned. It sounds like you really need to find out why Nathan is having moyamoya symptoms, and what the plan is if blood flow is still very compromised.
I'm sorry that you and your son are going through so much. I know how scary this disease can be.
Jenny