its no problem
If you insist on running a dual muffler setup from the factory y pipe than ok. But if you are wanting to run true duals I would recommend doing a h or x pipe. (muffler shop should know how to do this) than go to a muffler on each side. From my understanding with your motor is that true duals will be confusing the hell out of your computer possibly throwing a code. Unless of course you get a tune that turns it off.
Honestly, to save money and help out. I would a single in muffler and either dual out or single out. This way you don't have all the extra piping under your truck.
I have straight dual exhaust on my truck and it is a PITA and it runs along the passenger side. One thing you have to think about is that it needs to run along the passenger side as your gas tank is on the drivers side and takes up a decent amount.
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