Interestingly enough, the new (July 2011) American Rifleman has a long article entitled "Guns of Manassas - 1861" There is a lengthy description of the guns available at the Federal and State Armories at the commencement of hostilities.
The early issue arms ran the gamut from flintlock muskets to the 1855 rifle. Included in the armories were many 1842 muskets and rifled muskets, fewer 1841 'Mississippi' rifles, some 1808 and later flintlock and converted muskets, some Hall's breech loaders and in one case Colt Revolving Rifles.
There is a lot more in the article, it's a great read. G