The differential vent you asked about was probably bolted to the bed itself for clearance away from the passenger side tail pipe, stock it was bolted to the frame right in the path of the passenger side tail pipe. As long as you keep it up high or put it back on the bed like it was it will be fine.
Here's a pic of mine. notice where it goes up to the frame... yeah it was moved for exhaust. as long as it's high up and won't get burned you'll be fine.
