and exhaust shouldn't do anything because technically your not fooling around with your engine--but toyota dealerships are known for being dicks.
what i would do is take it in to them and see what's up--its really not worth taking your Intake
and exhaust off for such a simple problem, so if they do NOT cover it because of that i'd just buy them and do it yourself..it's pretty easy. of a scale from 1-10 i'd give it a 2--and that's only because you've never done it before. otherwise i'd give it a 1
but really...i hope they cover it cause it'll save you some hassle...just keep your fingers crossed and hope you catch them in a nice mood.