I would not discount the "scurvy" diagnosis so quickly. According to "What Did They Mean By That? A Dictionary of Historical and Genealogical Terms Old and New" by Paul Crake, J.D., pages 263-264

"Scurvy: a disease causing painful joints and mental apathy. peculiar to mariners, recognized and cured from earliest times, it nevertheless likely affected as many as 30,000 men during the American ivil War."

"The Encyclopedia of Civil War Usage" by Webb Garrison, page 221

"scurvy: a nutritional malady caused by a lack of vitamin C due to a lack of fresh vegetables and fruit. ... it became a major illness among the soldiers of the Civil War during the last year of the conflict. Scurvy causes spongy gums, loose teeth, and bleeding in the skin and mucous membranes."

JR