Im Having A Problem With My Mustang!!! Need Help

Well I just install a JLT Short Ram with the heatshield on my 2002 Mustang GT, after I install it I did a couple of runs around my block to feel the new upgrade, everything was good until, 2hours later the "Check Engine Light" came on, later on that day I was stop because I was waiting for the train to pass, and all of the sudden my car was acting weird. Like it would idle a lil below normal and sometimes it would idle at 500rpms or lower (about to turn off), the car would also shake a lil bit too and later on that night I would hear like a noise coming from the engine like clicking noise (best way to describe it) but it would do it after a while. Could this possible be because of the new intake? I mean i put right where it suppose to be and there is really not much to plug back in, except for two hoses and the MAF wire. And I recheck and even use cramps on the hoses so they wouldn't come out loose. So

what could the problem be???

But why would my car start to idle like its about to turn off? and idle really low? at 500rpms or lower. I mean the JLT intake i got was from americanmuscle.com and didnt read no complains about it. Could it be spark plugs? or something similar? I hope its not something big. Does the codes u were talking about has something to do with that?