From a thread on Yotatech:
MAGNUSON MOSS WARRANTY ACT
US Code - Title 15, Chapter 50, Sections 2301-2312
Legally, a vehicle manufacturer cannot void the warranty on a vehicle due to an aftermarket part unless they can prove that the aftermarket part caused or contributed to the failure in the vehicle (per the Magnuson Moss Warranty Act (15 U.S.C. 2302(C)) . For best results, consider working with performance-oriented dealerships with a proven history of working with customers.
From:
http://www.magnusonproducts.com/magnusonmoss.htm
The farther you get away from the modification, the more difficult it would be for them to prove a connection. However, that doesn't mean the dealer will fix it. It may require arbitration.