You might want to consider getting something like an UltraGauge to monitor your fuel trims. It's relatively cheap and a good way to make sure you aren't running super lean.
http://www.ultra-gauge.com/ultragauge/index.htm
You're probably running in the upper negative teens to low 20% range for your long term fuel trims, which isn't so good in the long term. A stock V6 airbox will usually have LTFT reading from -1% to 4%. Chances are good that the Y-pipe is actually messing with the MAF readings and meter MHz scaling. While the increased MPG is a nice thing, chances are you aren't helping prolong the life of your engine.