Yes you should... and now that i'm looking at your setup, I'll soon be having something similar to yours... i've ordered the AT4040 to put in front of my 30" magnaflow muffler. which is a straight thru design. when I added the mag muffler, I lost alot of low end torque, upper end hp went up and it breathed really well past 3k rpms. since I dont race my truck and I dont tow, i'd prefer a balance of low end performance & upper end performance.
my goal is to get a consistant 17 mpg average with plenty of power on tap for when I need it or want it.
as far as the ATS intake goes, I recommend it.