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You have an interference motor. If you had to replace the heads due to the valves possibly touching the motor, you have to consider rechecking the compression after you replaced the heads. I had the same motor that had an intake leak. I found frozen rings on the number 1 piston as well as a bent pushrod. Ultimately, the camshaft had broken due to coolant getting to the bearings. If the spark is good, the fuel is good, then the only other problem you'd have would be compression.
It sounds like it could be a bad coil pack that is used for number 5 cylinder. It could also be a bad spark plug wire. Does the weather seem to make a difference? Try this quick check once night time comes around. Open the hood and start the engine. Fill a bug sprayer with salt water and spray the plug wire while the engine is running. If the wire is bad, you might notice an electrical arc from the wire to the engine block. The engine will probably start running rough. If this occurs, then the wire should be replaced. If it doesn't, then the coil pack can be tested with an ohm meter. I hope this information has been helpful to you. Good luck with your problem and thank you for using Fixya.com.
I had this same problem on mt 2004 jetta. It had 85,000 miles on it. one day it bagan to idle rough but seemed fine when at higher sppeds/rpms. after a weekm I took it to the dealership and it turned out that a few of the coils/springs were shot. they also replaced my spark plugs, costing me about $550 total. But the car runs great again.