NO, changing the Dist. Cap will not mess up your timing. that only comes into play when changing the distributer. Unless the bolts are not tightened, then you could mess it up...which im sure that isnt like that. I am pretty sure that the fuel filter is in the same place as 4th gen, so not too hard.

YOu could also get some Seafoam Cleaner for your Throttle Body. Its easiest found @ NAPA. Its in a tin can, and the can is white. its called deep clean or something. You just take this, and with one of the vacuum hoses that you took off when you put in the CAI, just put the hose back on, and you get the car up to normal temps, and just suck a little through the hose(cuttin the tip of the hose is the easiest way to do this, like @ 45 deg. angle. ) And you should suck up about 1/3 of the bottle. then just put the hose all the way in, and it will stall out. wait for at least 5 min. to let it soak in. Start it back up, and it may take a couple trys, and just let it sit and smoke all the shit out the exgaust. make sure you are outside when you do this, it will smoke for a while.

I did this on my 4g, and it ran ALOT smoother