My neurologist ruled out ms, lyme, vegative disorder, etc. just by checkin reflexes, etc. etc. and a brain scan done 2-3 years ago. is this accurate?

Probably: History and examination make up most of what we do and how we figure out what's going on. Imaging studies are to confirm a diagnosis, not make a diagnosis. If vegetative state is something you're worried about i wouldn't be worried if you're posting a question here.

If you have doubts: Get a second opinion, as sounds like you have little confidence in your current doctor.