Also if you want to mod without potentially hurting your warranty you may as well not do anything in the first place, some dealers will find any way to say xx mod caused this to happen so sorry you lose.
Are you saying they TOTALLY VOIDED your warranty because of the mods you have (MSP CAI, Geddy RS BOV, and Magnaflow mufflers) if thats the case i would fight that because mufflers dont cause problems MSP CAI is made by aem/mazda and there bov sucks anyway. I sure hope theres some other factor...