Regarding black troops engaging in combat against Missouri Confederate guerrillas, I am unaware of any such occurance. The closest situation I am aware of is in September/October of 1864, when Confederate guerrillas Bill Anderson, George Todd, etc. were making themselves known in a major way in north central Missouri. A colored unit, thus far unidentified, that was apparently being recruited is known to have been taken under the command of General J.B. Douglass in order to defend Mexico, Mo., against a potential guerrilla attack. Note that this was in the immediate aftermath of the Centralia Massacre and in the midst of Price's Raid, and most front line U.S. troops in the area had been diverted to the defense of Jefferson City, leaving wide swaths of the area the guerrillas were operating in undefended. Under the circumstances, these USCT troops in Mexico likely would have engaged in some sort of patrolling into the countryside. As of yet, I find no evidence that any contact was made. Several other USCT regiments were recruited in Missouri during the course of the war. However, they were recruited during times of less chaos, and while other Federal units were in the vicinity would have been available to patrol, making USCT/guerrilla contact less likely.

Regarding black EMM units--no such thing. EMM units were generally raised by county, and generally included all local men between 18-45 who swore the Oath of Allegiance. No seperate but equal EMM units. Your question does raise an interesting issue--did free black men serve in the EMM? What about male slaves? While it is highly unlikely that slaves or free blacks served in the EMM given the segregation of regular units (no reason at all to believe an exception would be made for the EMM), one avenue of research would be to identify free blacks from the 1860 census, identify their area of residence, identify the EMM unit associated with that locale, and then look through the appropriate EMM muster lists for the identified names. Slaves would be much harder to research in this manner, since they were not identified by name on the census reports.