98 Mustang GT running rough

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I have a 98 Mustang GT with 96,950 miles. It is automatic. I maintain the car meticulously. Oil used is QS Advanced 5w30....just completed an auto-rx treatment. Tranny fluid was changed a month ago.I've had a problem with my BBK Under drive pulleys causing my serpentine belt to "glaze". The belt is making a little noise. The UDP's are piggy back style.....they use the existing harmonic dampener....I dont think this could be causing the harshness but i have replacement pulleys on the way because I want a one piece design. When i first start up the car it idles rough...It never did this before...If i look under the car i hear tapping coming from the bottom of the engine and i can literally see the H-pipe rattling around (it is not loose). After about 20 seconds the tapping stops and the engine runs rough. I replaced the plugs last month and the wires about a year ago. PCV valve is also about a year old. Air filter brand new amsoil eaa..02 sensors brand new.....just cleaned throttle body and there are no vacuum leaks. Its driving me nuts. Can the pulleys or a slipping belt cause this? I think it is the wires but i dont want to spend 100 bucks for no reason. I also cleaned the idle air control motor but it is still doing it.
 
Have you scanned it for codes? Are there any?

A leaking EGR valve could cause a rough idle, but there would normally be a code for excessive EGR flow if that's what's happening.
 
have heard about the EGR lines clogging with carbon. might want to check your lines and see if they have any build up.
 
Before you buy any parts, pull codes and look for any P03XX codes. I have seen bad purge valves from the EVAP system, vac leaks and ignition problems cause rough idles on those. Never have seen an EGR cause a rough idle on any 4.6 , yet, but there is a first time for everything. As brianl703 said you will get an "excessive EGR flow" code if the valve is hanging open. Pull codes and go from there.
 
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