With the little experience i have on the subject, ill give my opinion.
You must get a 170 thermostat, Gutting those cats will make a world of difference and you will get more results from the tune.
If you planning on a few more minor mods IE: Headers, Throttle Body, CatBack, get that first then get it tuned. It will save more money in the long run.
If you want to just get a tune for your CAI, im sure Sean Roe has a tune already ironed out for the common mildly modified truck. But without a doubt, if your going to invest in a tune, you want something with big results. But be aware aggressive tunes increase risk. Getting one custom dyno'd for your rig can ensure safety. and a more precise a/f and timing tables.
If you plan on racing it often (careful, expensive shit breaks and wears out) you may want a higher octane tune. But i would go with a setup for a higher octane than 100. There is C16 and 118 octane available in most areas for bigger gains. This also merits, more attention to safety, and again i would encourage a custom dyno tune with the fuel in the tank.
If your not going to race it but occationally, and dont see yourself buying your expensive local 100 fuel often, you may only need the street tune. I dont know of too many people that swap between their tunes if they are not running race fuel.
I like 3 tunes. (1) bad fuel or Economy tune (2) 93 octane tune (3) 118 octane. But seeing as i wont be at the track anymore but 3-4 times a year. Im just going to get a single custom street tune.