Howdy,
The Civil War Soldiers & Sailors database system at www.itd.nps.gov/cwss/ has 26 J. to John A. Thomas combinations for Texas Confederate units which means you probably need to narrow down the field by obtaining a copy of his approved Texas Confederate pension application # 09773, which he filed in Bosque County. Pension applications had varying amounts of information but should include some details on which unit he was in. You should be able to order a copy on line from www.tsl.state.tx.us/arc/pensions/index.php . His wife was also approved for a widow's pension # 20152, also filed from Bosque County.
Bobby