The muffler delete does not hurt your valves and shouldn't effect your stock tune...
From what I have read...
I am considering changing exhaust on my 07 427R, have you checked out the Roush Extremes? They run a straight through "muffler" under the car with a long tail pipe, they sound old school awesome...
07 Roush 427R, Brembo 14" rotor and four piston calipers
05 GT Mustang, FRPP, FR X pipe, Hurst short throw,
American Racing Torque Thrust 10X20 wheels,
Granettelli tower brace, custom painted flat black grafix, Yellow Optima