My trucks done this to me as well if Snow/water gets into the Coil or distributor cap. The heat from the engine however just evaported it after some driving.
By any chance, Once you hit a certain RPM does the cylinder start to work again? At idle, mine would shake BAD and sound pretty sweet, then at 1500-2000rpm the Cylinder would start to fire...then when going to stop..it would go back to the rough idle. After a few revs (upto 4500 or so) and maybe 5 minutes of driving, it went away.
Did any water at all come out of the distributor cap or anything odd like that?