Noise Unknown

I just recently purchased a `93 Cobra and it runs excellent. Well I shouldn't say excellent I guess because the #2 plug wire was melted on the header, causing a huge miss. Problem is that I just changed the plugs from the regular Autolites that were in it to Autolite Platinums and put new MSD 8.8's in it and now it sounds like there's a rocker slappin' up against the valve cover on the left, passenger, side of the engine. The new plugs and wires fixed the miss and throttle response is unreal, but what's with the noise? I felt the valve cover and there is nothing hitting up against it. The only thing I could figure is that there is something wrong with the #2 cylinder for having that bad plug wire for however long. Anybody have any ideas on what the problem is? Any help is appreciated.

Thanks guys! I'll check into both of your ideas.