Jeff; I've thumped around in all my usual places and don't turn up anything new on John Riley Thompson.
Having read the biograpy from So Ill. on his son I think the reference to his raising a company refer to his steamboat days that are clearly post war. If he was river piloting at the time of his second marriage that would account for the moniker "Captain" on the marriage record.

Interesting fellow in any case.

John R