A good "rule of thumb" answer to this age old question is if you're not messing with intake air or fuel or the cats, a simple muffler swap rarely effects the bike's running condition negatively to where it now requires a "tune" (getting the mix back just right). Note this question is usually answered by vendors and service departments in another way - because muffler change or not, tuning never hurts, because any of today's bikes will run cooler (and better) from a richer mix (more fuel at the expense of higher emissions); more importantly, that "other" answer ALWAYS provides a sale and a profit. Put the pipes on...leave the air box (and filter) alone and as David said it will (more than) likely be just fine! That said...once product is on the market a most excellent next step is eliminate the cats, by-pass the flaps, feed it more air and more fuel and get a compatible tune. The last part is the ONLY reason I miss carbs... increase the air, change the pilot jet, raise the needle, improve the slide spring, increase the main jet, increase the air, fine tune by reading the plugs and call it a day!