no a 40 series will not work for a muffler replacement, in 08 to present titans its a dual in single out replacement muffler. so you either need a dual in single out like lvcoyote suggested the 2.25 inlet pipes and idealy 2.25 out unless you want 3" pipe to the rear its 2.5" out of the the stock muffler i believe. Flowmaster makes a 50 series muffler in this configuration. if you really want a 40 series you will need a y pipe and a little pipe join the 2 pipes off the exhaust manifolds into a single pipe to the muffler. then what ever size you want out the back.
I got a cheap dynomax cat-back system first. I didn't really like the sound so I got the 50 series. Didn't like that either and got the super 44. Still really couldn't hear it to my liking so I ended up getting the dynomax bullet and dumped it before the rear axle. Best sounding exhaust I've found and others around here agree (even die hard Ford fans).