Here are a few suggestions. I would give a little time, sometimes the ECU takes a little time to adjust to certain mods. I would also look at this thread.
TRD Duals vs. Banks Monster Exhaust It does make a few mentions about magnaflow, but it a great source of info for anyone looking at exhaust options.
I would look into these alternatives too, if you are at 30k or more without service you should replace spark-plugs, clean throttle body, clean /replace air filter and clean the air box. This will ensure peak performance. I doubt you are at this level just because your truck is still relatively new. (but just in case)
As far as mpg calculations go.
1) Fill up your tank
2) Set your trip meter "A" to zero
3) Drive your truck until you get say down to a quarter of a tank or any milestone you want. I would do the qrt tank for mixed driving, and 10-15 mile run for all highway..etc
4) Fill up your tank again & Look at the number of GALLONS you just pumped to the "hundredth decimal place" (not the cost)
5) Go to your trip meter "A" and get the reading (assuming you didnt monkey with it since the last fill up)
6) Divide the amount indicated on your trip meter "A" by the number of gallons (to the hundredth) you just pump - Use a calulator to get an accurate reading (I doubt you can do it in your head)
7) Thats it!
(if you have bigger than normal or smaller than normal tires this will effect your performance)