2006 Jeep Grand Cherokee engine noises

I have a 2006 Jeep Grand Cherokee with 22,700 miles. I started getting an exhaust leak at about 13,000 and the dealer finally (after 4 or 5 visits) discovered a leaking exhaust manifold gasket and replaced both gaskets. This eliminated the leak. Since then, I've installed a Flowmaster muffler and a K&N 63 series Air Charger air intake system. I'm getting another noise or collection of noises that sound similar to an exhaust leak. Its not present at idle or while reving while parked. I get the noise in all gears, but is most noticable under load/ acceleration in 4-5th gears. I went back to the shop that installed my muffler and they couldn't find any exhaust leak (using a stethoescope). I've read that installing a cold air intake such as the K&N will increase noise from the EGR valve. I've thought about re-installing the factory intake assembly to see if this is the cause, but haven't yet. I've also thought it might be valve or lifter clatter and tried to quiet this with Valvoline SynPower Oil Treatment. Can you offer any suggestions or other potential causes?