STK 4X4

i have a 97 civic ex. have minor bolt on's. i have noticed when i am at a stop light when i have my foot on the brake pedal it idles a liitle rough. when i let my foot off it goes away. i have also noticed when i drive a little harder reving it a little farther till i shift it will idle rougher. any suggestions. also i have a VAFC and my vtec ingagement is set to 4500. is this to low. i didnt' set it, i chose not to mess with it cause i don't want to risk messing something up to bad.