I see two potential problems here.

1) the initial virus, sounds like a form of hepatitis, from the symptoms you describe. Were you tested for liver functions?
Were they elevated? Not all hepatitis is A, B , or C. There are general infections that may occur from other viruses, but they are usually temporary. There are tests for the A, B, and C variants, and those would show antibodies if you have or had one of those infections.

2) Flagyl is metabolized by the same enzyme system as alcohol. That is why a sticker is put on the bottle by the pharmacy to AVOID ALCOHOL. People can inherit an inability to metabolize this drug, and therefore aldehydes build up in the system. These cause all sorts of symptoms similar to Antabuse (alcohol deterrent)
drug which shares the same system.
These are the symptoms of aldehyde build up in the body:
from http://alcoholism.about.com/od/meds/a/antabuse.htm

Flagyl can also cause lesions in the brain. This complicates things for diagnosis considerably. They can resemble the lesions caused by MS. They only show up on MRIs.

I hope the specialist you have found is Dr. Latov, or Dr. Chin, in NY.
Some of our PN posters have been to one of them, with favorable results.

We had a poster Beglet, here who claimed to have gastroparesis from Flagyl... she no longer posts here sadly.

Autonomic neuropathy can affect the stomach, blood pressure, and heart, if the nerves that supply them are damaged by a toxin or infection. It is tricky to diagnose. Sometimes there can be triggers in the environment that set off autoimmune diseases, like Sjogren's or lupus. So I think you will have to wait until you see your specialist.