pants and jackets were wool.
pants were held up with suspenders.
shirts were usually linen or linsey-woolsey, a blend of linen and wool.
cotton was too expensive for most soldiers to be able to afford.
levy soldiers (volunteers & "draftees") wore what the had on when they were pulled off the farm or town streets.
actual soldiers at the time the war started (and periodically throughout the war) were issued Brogans - a short lace up type boot, most similar to a chukka or boondocker type boot. (slightly above ankle high) Cavalry soldiers had mid calf to nearly knee height pull on boots often called "mule ears" because of the leather loops sewn in them to make it easier to pull them on.
Most shoes/boots up to the civil war were made identical - you had to wear them in to get them to fit left or right.
There were fabric mills to make the raw cloth, and a lot of uniforms were machine sewed, but "homespuns" were hand spun, woven, and sewn - which is what most farm folks had to wear. "Store bought" clothing was a luxury item.