You DO have choices, in spite of RIZECUSTOMZ's glowing recommendations for the Gryphon. There is the XCal, which is a good programmer and VMP and Troyer Performance are good people to talk to if you want to go that route. (Here at PHP we recognize we're not the only game in town, even though we think we're pretty good). Sorry - I'm just a fan, but I know Bill and Corey would say the same thing - it's all about what YOU want , not what somebody else wants for you.
Now, back to your question. Your truck COULD have a program in it. There's no way for you to really tell. It sounds like the speedo was off with factory tires and gears - if so, that might be an indicator that it has a non-factory tune.
E10 gas is pretty much the standard blend everywhere. I'm pretty sure any tune you get will account for that.
A programmer such as the Gryphon will let you adjust your speedometer so it shows the correct speed, regardless of tire size. You should gain a significant amount of power (if you ever need it - like in passing). You should see a gain in fuel economy.
If you put in a CAI, you will definitely want your truck tuned for it or you will risk running lean. The exhaust mods should not be a factor.
I have a Gryphon on a 2005 truck that I, too, bought used. It is the BEST modification I have. I would not be without it.
- Jack