2000 cavalier is making a flapping noise after changing the spark plugs, the noise seems to go away at faster speeds but comes back when stopped or slowing down. it seems to be coming from the engine.

Don't drive this vehicle unless you are going directly to a mechanic because some of the possible causes for this noise could do more damage.
More information please. Use the comment button below. What exactly does the 'Tapping' noise sound like and when does it happen? Does it get faster when you press the accelerator? Does it only happen when your moving?
If it does not change speed with the accelerator it is not likely to be an engine issue. If it only happens when you are moving it is possibly something on the transmission or the drive shaft setup.

First I will change the spark plugs, My BA Ford in Australia was like that, totally different car with new spark plugs

OK. The noise you are hearing is the recirculation flap motor. It could be what is causing the condensation. Easy way to check in after the noise has stopped push the recirculation button on the AC controls to see if the noise happens. If the motor is bad and the flap isn't closing you could be getting moisture from the outside air. As far as the check engine light goes there is no relation. 2 completely different systems. The flap motor would probably run you a couple hundred of dollars. The check engine light could be anything.

look for loose mud flaps. check under the front of the vehicle as there is a plastic panel from under the radiator back to the front cross member. This is light weight plastic and held in position by small plastic plugs/clips Hitting something on the road (small bird-- clump of rag or parking over a tire stop in the parking centre )will break it and it hangs down and flaps as you drive.

Fix your car right away by clicking the link I attached Chevy Cavalier 1995 2005 Factory Service Workshop repair manual

sounds like the wheels are out of balance, is there a slight vibration through the steering wheel at this speed? and does the problem stop if you go faster (please drive carefully)

How much exhaust is coming out, sounds like a collapsed muffler/clogged catalytic converter. Run it for about 20 minutes in your driveway, being careful, NOT TO TOUCH components. Move your hand from rear to front, it should feel about the same amount of heat coming off all the rear most pipes. Very hot toward front. If a blockage, as your hand passes over the parts of the system, you will feel a difference.

it is probably your transmission

Just change the compressor it is easier than changing the clutch if you do dont forget to change the reciever dryer and the orfice tube and have a evacuation done on it.

either your fuel filter by be plugged, could be injector shorting out could be throttle position sensor