I just noticed the Trans Mississippi OOB and setup for that scenario is rather problematic. Historically, as far as I can figure, the situation was as follows.
The Union controlled Jefferson City, Rolla and Springfield in addition to the current cities, I'm not certain about Charleston.
The Confederate Army was at or near Carthage Mo and was organised as follows:
Jackson's Column
BG Stirling Price
Rains' Cavalry (BG Rains) (8th MSG Cav.) (100%)
Mo Bty (?) (Mo Bty)
2nd MSG (BG Rains) (2nd MSG) (100%)
3rd MSG (BG Clark) (3rd MSG) (100%)
Rives' Cavalry (4th MSG Cav.) (50%)
4th MSG (BG Slack) (4th MSG) (100%)
6th MSG (BG Parsons) (6th MSG) (100%)
Note: percentages are of strength, meaning Rives' would be understrength), the 4 numbered MSG units are Militia.
Union forces were at least in two places:
Lyon's Column at or near Jefferson Mo
BG Nathaniel Lyon
1st Mo Brigade (Maj. Sturgis) (2nd Mo, Bat 1st US, 2nd D US Artillery (65%)
3rd Mo Brigade (Lt. Col. Andrews) (1st Mo, Bat US Recruits, Du Bois Mo Bty) (65%)
1st Ks Brigade (Col. Deitzler) (1st Ks, 2nd Ks, 1st Ia) (75%)
Sigel's Column at or near Springfield Mo
2nd Mo Brigade (Col. Sigel) (3rd Mo, 5th Mo, Backof Mo Bty) (65%)
Note: It might be worthwhile turning all the Mo, Ks and Ia Infantry into Militia (most or all were 3 month regiments). The Union also had some regular cavalry, but I'd factor that into the strength of the two regular battalions. I have no clue about other Union troops at Saint Louis or North of the Missouri river. Lastly, some of Lyon's Force might also be at Lexington.
All of the above is largely based on presence of troops at the battles of Carthage (July 5 between Sigel and Jackson) and Wilson's Creek (August between Lyon, Sigel and Price). I am certain that Jackson had already evacuated Jefferson City, Rolla and Springfield by early July.
Edit: I forgot to mention that none of the above forces should be locked as the battle of Carthage took place during that first turn.