you should get custom tunes ASAP! the tire size isn't going to really change for the tunes, and yes you can change the TS after the fact. I have 35"ers on my truck and all I had to do was change it in the gryphon menu.
Get the custom tunes to fix any possible lean condition the CAI has introduced. and honestly you may just want to sell the CAI and do the gott's mod. no lean condition exists from it and dyno's have shown that it does almost exactly the same (performance wise) as the couple hundred dollar CAI. you could then sell the CAI to help pay for the programmer...
Hope that helps!