Humphrey Marshall's army was in Mount Sterling on the 25th, on its way west toward Perryville where it saw no action but got close enough to hear the artillery rumble. Morgan's force fleeing Cumberland Gap were on a northerly route and crossed Marshall's path only a few days after the Confederates. Thomas Johnson's 2nd Mtd. Rifles, part of Marshall's command, were probably acting in concert with Jno. H. Morgan's and Jno. Shawhan 's cavalry units in chasing Morgan's Union men. A note was made on the 25th at Mount Sterling that Jno. Morgan was dispatched to search for the Unionists. It's a small wonder that your ancestor lived to tell about it and that he wasn't killed in retaliation for an incident at Licking Station (Salyersville) on the 15th. Marshall's men captured a Pike County Home Guard leader and some 30 of his company and held a field court martial and condemned the leader to death, but the gentle natured Marshall rescinded the sentence. However, some of Marshall's men weren't so kind and offed the Unionist leader before the day was over. The deed was attributed to some "avenging" force. The Home Guards had probably been on point for Morgan's Unionists fleeing from Cumberland Gap since their leader had been associated with the 14th Kentucky Infantry US for quite some time and the 14th was part of Morgan's C'land Gap command. I realize this doesn't help much with your ancestor - too many Morgans - but it broadens the perspective of his capture.
Randall Osborne