It would make more than a 2.8% difference. You need to look at the difference in revolutions per mile on the tires not the sidewall height.

I'm not saying it is all the difference you are experiencing but could account for 1-2 mpg.

I could do the math and post it but I just don't feel like it today!

 

Here is what my take and opinion is from the original post.
1. The airaid may have required the tune to keep the engine from going lean with that intake setup.
2. Gutting the cats suggest the program has elimimnated the rear Ox sensors operation because normally the cat efficiency test would be failing from "no cat guts".
3. Did the tuner change shift and lockup points?
4. Your running a modified setup in a way it was not intended, now.
5. Do you have the stock tune so you can go back? If not, you could be in a jam if the PCM ever has to be reprogrammed or you sell the truck and the next owner want it stock again.
Lastly, baseing performance on just a few miles a day is not my idea of real time performamnce measurements for anything and I would need more convincing about the tune effects. You had no before and after to compare with.
Gutting the cats did absoluely nothing for performance so there was a number of things done that are of questionable value and will cost a bundle to replace back to stock.
My position is the Airaid and other intake systems never do any good either for their high cost. On a race truck maybe but not when there is eggs between the foot and the electronic throttle pedal.
Last evening on my stock 02 4.6 I knocked off a 17 mpg on a run.
I think you should have thought a bit longer before buying this truck.
What were you looking for with it? To many questions need answers now.

Good luck.

 

Yes, the "squish" factor can be a player, and if the OP had installed 35" tires or larger, then I'd be more inclined to agree. However, for the new tires to decrease fuel economy by 1-2 mpg (which would equate to 9-17% decrease in the OP's case) due solely to odometer error caused by "squish," the differences between the tires would have to be much larger than 2.8%. Decreases in fuel economy as high as what you mentioned would be more likely due to a higher rolling friction factor (RFF) for the new tires. (I'd be willing to wager the Toyos--even at the OP's 50 psi--probably have a higher "squish" factor than the stockers, anyway, which would actually put them closer to the rolling diameter of the stockers.)

I have a relatively long commute (13 miles), but I'm fortunate that it has little traffic and long straightaways between just a few stop lights. I've been reliably getting high-16s/low-17s (hand-calculated) on my commute. But even then, the first several miles I drive in the morning cause my overall fuel economy to drop--it's only the last half of my commute that I make up the difference. The reason? My truck needs to warm up and, until it does, my fuel economy is going to be lower. If my commute were only 4 miles in stop-and-go traffic, my mpg would be nowhere near what I'm currently getting (and I know this from experience with short, high-traffic commutes). And yes, my truck is in excellent mechanical condition.

If someone knows a tuner who can make my truck warm up faster and also get better mileage while my truck is idling at a stop light or fighting stop-and-go traffic (i.e., without running my engine outrageously lean or forcing me to carry around 1500 pounds of batteries and plug it in every night), then please let me know. I'll be the first in line with my cash in hand.

Cheers, everyone!