Judy, except for suggesting the alternative of seeking professional assistance, I can only add one thought to the suggestions I made in message 15633 on August 31, 2005 in this forum.
You say that you, "checked with the county clerk, in the county where Ft Sam Houston Tx is located". That would be, I believe, Bexar County? His enlistment info contained in the Archives says his place of residence at enlistment was Nueces County, TX. If he returned there after the war, he may have recorded his discharge in public records there, rather than Bexar County.