What is the size of an unported Gen III supercharger inlet? I know they usually get ported to ~75mm, but if it's unported it would still cause a "bottleneck".

With the LQ4 MAF, check the classifieds here I puchased mine from a fellow member doing a demod reasonable. And yes, headers/exhaust work should be done before or same time as mods. If you introduce more air into your motor, you have to free up the path for it to get out.