Whew! You sure took me up on the question department, didn't you?
I want to be sure I understand: If you tow, you're towing something in the 6000# range, right? As long as you stay fairly close to that, say +/-1000, you're fine with a single customized tow tune. If you were to "regularly" tow something in the 3000# range, I'd probably get a second tow tune for that.
Now, the other tune(s). You'll probably find, like I did that you only need one. The one that works for you when you're not towing. I'd call that the daily driver tune. Unless you are in the habit of going out on Saturday nights and challenging young bucks to drag races off of stop lights, I don't think you really want a "performance" tune of that nature. The daily driver tune is your performance tune. Just tell Bill what you want from it, i.e., good passing performance, improved fuel economy, "reasonable" power out of a stop, nice shift feel, etc. (My vibes are telling me this is kind of where you're at - if not, tell Bill!)
So if you only end up getting two tunes, don't fret! That's one more than Ford gave you!
The tranny tune mostly makes the transmission work better. I don't know if it does much else. Its improvements are included in the other tunes.
Bill's custom tunes DO take care of all the major stuff, including Tire Size and Gear Ratio if you tell him what they are. You change things at your own risk. If you'd like him to change the speed limiter, tell him what you want it set at. He'll set the shifts and the max RPM. Following instructions is always a good idea.
I don't know of any way to "save" your tunes on your hard drive. I understand your concern, but Bill can always put them on the server again if you need them. They have to be loaded through Pegasus.
- Jack