I'd start with Missouri Boot and Shoe or Robert Land. Mattimore Harness is right up there too. I think most would agree they're among the best makers around today. Yes, your are correct. Pegged soles cost the government more per pair than sewn soles. And, without actual documentation, I'm pretty sure sewn soles were more common.
"Grumpy" Dave T.
"Yet, despite these small numbers, Kernstown was one of the most decisive engagements of the war. The Confederates, Under Jackson, though soundly defeated, ultimately lost the most. As historian Bruce Catton observed: ‘The victory meant nothing at all, whereas the mere fact that the battle had been fought meant a great deal.’ Indeed, the ramifications of this odd little affair reached all the way to President Lincoln."