SixBanger is right. Federal law says a dealer cannot void your warranty because of aftermarket parts. They can only refuse to fix the problem under warranty if they can prove that an aftermarket part was the cause of the problem.
1966 Mustang Sprint 200--Wimbledon White
1998 Mustang V6 Coupe--Silver--RIP, Totalled by brother
2005 Mustang V6 Premium Coupe--Sonic Blue