First, like everyone else has said the only way to calculate mpg accurately is to write down how many miles per tank and how many gallons to fill it up. Or use an app that does the same thing. I reset the mpg calculator every time I fill up but only use it as a guide as I have an Excel spreadsheet that I track my mileage with. The on board calculator tends to be conservative.
Second, just putting a high flow muffler on isn't going to be noticed by the ECU or the knock sensors. Resetting the ECU isn't going to change you mpg. It will lower your back pressure which means you will lose some low end torque. How much this affects you mpg is based on what size engine (V8 or V6) and how you drive. If your calculator is indicating lower mpg and you are driving conservative then it means your engine has to work harder with the loss of low end torque.
There are no performance chips for Toyotas. There are piggy backs you can wire in and tune your fuel maps to optimize you power but for bolt ons that is usually a waste of money. My thoughts are if you want to make your truck louder invest in a quality cat back. You may still lose some low end torque but they are at least dyno tuned to produce power to help compensate for that in the mid to high rpm range. Otherwise high flow mufflers are all show and no go. And I base this information on having a custom built header and exhaust on my MR2 with dyno graphs before and after. Also, just putting a high flow muffler on an 04 Corolla I could feel the low end loss. For my 06 V8 4Runner I left everything stock so far because I tow and losing low end power is not an option for me. That and it is my road trip vehicle and I don't want all that noise for hours on end.
In short, if everything else is the same and only the muffler was added then you have to decide if the loss of mpg is acceptable for the sound or not.
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