Go and see your selling Ford dealership and speak to the service manager. I saw my local dealer and he said my proposal to fit Pacemaker extractors and 2 1/2 inch system would not void my Ford warranty. (Of course the exhaust system would no longer be covered by warranty). They were interested in who would be fitting the system (the particular fitter was well known).
They offered to source and fit a full Herrod system (but I've opted to go with Paceys and a mild steel system for a fraction of the price).
I'm not sure if this is only a dealership response (as they do the warranty work). Best thing is to see the dealership and discuss the proposal before you go ahead.