--my first thought with a rapidly ascending neuromuscular disturbance would be Guillian Barre syndrome, or one of its variants, including a possible attach or re-attack of chronic inflammatory demyelinating polyneuropathy, an autoimmune waxing/waning entity that is related to Guillain Barre (it's often considered, the "slower", more chronic form of that condition).

The recent prior history of infection also supports that idea, as a prior infection can often set off the immune molecular mimicry that leads to the neurological attack and symptoms.

Don't know why the EMG results should preclude the lumbar puncture in a case like this either--especially if the EMG showed nerve compromise.

I'm assuming MRI's were done to rule out obvious spinal cord issues--was one done of the brain as well? Often, in cases like this, another possibility is MS or another central nervous system demyelinating disease, such as acute disseminated encephalomyelitis (ADEM--these are distinct from demyelinating conditions of peripheral nerve such as Guillain Barre).

It really sounds like you need to get him to a (better) teaching hospital. The problem now, though, is that with Guillain Barre and similar syndromes the initial attack may be over and there may be less evidence to find, even if there are residual affects; has he improved?