Gary, a Thos. Jefferson Howell filed a pension application in 1910, listing his unit as the 20th Ms. The filing occurred in Scott Co., Mississippi. Not sure this was your Thomas Jefferson Howell due to differences in unit identification?
Pension applications were also filed for four Howell, W.'s and four Howell, Williams - none of which carried a 39th Miss Inf. unit designation. Let me know if your William Howell may have been reassigned to another Mississippi unit, under which name he or his wife filed for a pension application.