Its A 1996 Civic With 1999 Civic Swap Stock

Ok ive done pretty much everything to this car and the shaking wont go away and it seems that i lose power and my car doesnt run like its is suppsed to. I've changed the spark plugs, spark plug wires, distributor cap and rotor, fuel filter, air filter, oil filter, oil change, replaced both 02 sensors, and i still get low mileage, 23-25 mpg wtf is that!!!!. The only thing i do get is a cel code #54 CKF Sensor (Crankshaft Speed Fluctuation) can this cause all of those problems? Can anybody help me?