Anything you do to the truck for performance they are going to tell you that it voids the warranty (even if you install a K&N to replace the factory filter by the way don't waist your money on that). with that said I have a CAI from Bill Custom Intakes and have not had any issues at all. The tube that goes from the filter to the turbo has a diffuser in there you can remove that. cheep mod.
Tuners I am using a H&S Miny Max and again very happy with it if you want to eventually de-filter your truck look around there are still companies with them on the shelves and there is ways around it (the trans reprogramming is also worth it). I am removing my filters tonight when I get out of work EGR and cooler delete will be done next week.
Also I have heard that there a company called Green Filter they are supposed to be very good here are some sites to help you.
Research, Research, Research that is the key by the way all these guys are right if you want power you either have to go all out to get true power and performance