The Magnuson-Moss Warranty Act covered these issues. Here's a very good page on the SEMA site regarding aftermarket modifications and warranties:
http://www.sema.org/main/semaorghome.aspx?ID=50096

This paragraph is particular should be noted:
Federal law sets forth requirements for warranties and contains a number of provisions to prevent vehicle manufacturers, dealers and others from unjustly denying warranty coverage. With regard to aftermarket parts, the spirit of the law is that warranty coverage cannot be denied simply because such parts are present on the vehicle, or have been used. The warranty coverage can be denied only if the aftermarket part caused the malfunction or damage for which warranty coverage is sought. Disputes in this area usually boil down to arguments over facts and technical opinions, rather than arguments over interpretations of the law.