Problems at 3000-4000 rpms

i have an eclipse 98 non-turbo 2.0 L with 87k on it. Usually in the mornings when I first start the car, or whenever I start the car after a long period of time and when I go to first gear and second gear and hit 3-4000 rpms, the engine makes a louder than usual sound and then it goes away. I have no idea what it could be. i have an after-market cold-intake in it as well as an aftermarket exhaust. Am I making a big deal or is there a problem here? thanks