so it started at the same time as the cai? is the air temp sensor that is in your tube sealed up nicely? is the cone and tube clamped down nicely?
how many miles on the car?
the jerking to me sounds like something that happens when your tranny is about to go.
the vibration could be anything just about.

put the stock air box back on. if it goes away you know. if it doesn't you'll know its something else.