from what I have understood in reguards to warrantiesd and mods are that the only way a particular mod would void the warranty is if the "cause/root" of the problem stems directly from that modification that you did.
this is info that AEM put out abou there intakes and warranties:
http://www.aempower.com/faq.asp?fid=23&sid=4&tid=
Also further info from Enjoy the drive Powered by SEMA:
http://www.enjoythedrive.com/content/?id=8250