Looking at the index of the 1860 Missouri census I find these names of men or heads of families that could be your Elias Lyons:
--Eli Lyons in Perche Township, west Boone County (NE MO)
--Eli Henry Lyons in Hardin Township, Clinton County (NW MO)
--E. M. Lyon Syracuse in north Morgan County (central MO)
--Eli Lyon in Salt River Township, Knox County (NE MO)
Well, did I get the correct man in any of those? If not, please tell us in what Missouri county did they live by the 1860 census?

Here is why southern men kept getting in shooting scrapes at Monegaw Springs on the north side of the wide Osage River in central St. Clair County. When southern Major General Sterling Price sent out his appeal for southern men to come join his command in November 1861, they had to travel in groups by horse all the way to southwest MO and later all the way to Arkansas to be part of the southern response to the Union seizure of most of the rest of Missouri. Lots of these men organized around home under leaders with previous military experience in the Mexican War or whatever and then had that long horse ride to join General Price. The main natural obstacle was that wide, wide Osage River that was even then navigatible all the way from its mouth on the Missouri River near Jefferson City in the center of the state west almost all the way to the Kansas border. There were just a few good crossings, and Monegaw Springs was one of those. Naturally, the northern home guards or other Union soldiers of that area watched for groups of southern men trying to cross the river there and scooped up all they could catch. That is why there were a number of skirmishes at Monegaw Spring thoughout the war. The same is true for other notable crossing sites of that river.

Many of these prisoners ended up in St. Louis in the former McDowell Medical College on Gratiot Street which the Federals called "Gratiot Street Military Prison." At least one of my ancestors matriculated at that sad college during the war courtesy of the Yanks, and maybe more of his family but for lousy record-keeping we cannot really tell. The reason many of those men had no military record was that they were new recruits and their leaders didn't have time to write up any more than a roster with their names spelled in all kinds of ways, and quite often the man with the roster got caught, too, and the southern authorities never saw that piece of paper. Joane Chiles Eakins in 1995 put together many of those Missouri southern men who ended up in the St. Louis area military prisons from the National Archives and Records Administration microfilm files into an alphabetized list in a book, but I couldn't find an entry for either William or Elias Lyons or any similar spelling. The clerks in those prisons were not always the best with their record-keeping, either, and many men left no record behind.

I hope that helps.

Bruce Nichols