Ahhh, you left a HUGE part out of the story didn't you!
Yes, one of the more "common" causes of hepatits granulomatosis is an endemic mycosis such as histoplasmosis. I see you're from Nebraska, and I guess it makes sense that Histo is the dominant dimorph as opposed to Blastomyces, the dominant dimorph where I am from (SW Ontario, CANADA).
So you were treated with itraconazole for a year or so eh? It's kinda confusing reading what you wrote, because you said you were sick at one point and now have no symptoms. Were you having symptoms once you started on the intraconazole, and then they went away? Were you having fevers/chills/sweats?
You said you were producing the Histoplasma antigen--where did they find that? In your urine or blood?
Finally, whenever you find granulomatous inflammation, the diagnostic approach usually includes TB/fungus/sarcoidosis/lymphoma, and depending on which part of the body it is (like the liver) certain other conditions are added. They mentioned that methotrexate may have played a role. Possible--MTX is known to cause hepatitis, but interestingly, some cases of idiopathic granulomatous hepatitis are in fact TREATED with MTX! So, hard to know.
Another question: were you ever on any TNF-alpha inhibitors for your RA?