Alan...

I made it down to the National Archives last night and looked up Jonathan R. McDonald. He enlisted in CO H 9th Alabama as a private and was elected 2nd Lieutenant in June 1861. He was wounded in the hand at the Battle of Williamsburg in May 1862- the hand was so badly maimed that he received a dischrage under a surgeon's certificate in July 1862. There was no information about his transferring to another unit.

I have some more looking to do, but I think it's safe to say he made it home and eventually joined another unit. My gr-gr-uncle, John B. McClellan (a Lt. then Capt. of CO H of the 26th/50th AL), lost an arm at Murfreesboro and after convalescing at home, joined a partisan command in northern Alabama.

John