Brief Answer:
I don't think he had JC virus.
Detailed Answer:
Hello,
I reviewed your query and here is my advice.
The JC virus gives brain infections only in persons with low immune system.This means he could have brain infections if he is suffering HIV/AIDS, have chemotherapy, suffers leukemia or hodgkin lymphoma or bone marrow diseases etc.The doctors should have done an MRI to diagnose it and maybe a spinal tape.This infection may even be deadly.
The fact that stroke did gave him disabilities maybe was a transitory ischemic attack well managed .I dont think he had JC vurus.
Hope I have answered the question.
Let me know if I can assist you further.
Thanks.