Not that I am an expert in any of this, but from what I have read i might be able to help.
with the top speed of towing, I have never heard of a truck not being able to tow a boat at whatever speed was needed so I cant help with that, with the other two its not too difficult to explain i think
when you adjust the tire size in the programmer, it changes the computer, so both the speedometer on the dash, and in the gryphon will show the change. to get the correct tires size there are many different links and calculators that you can use from PHP that will get you the correct numbers to put in. I think Bill says the best way is to get how many rotations per mile the tires do, then divide a large number by that.
With the custom programming you just need to change your tire size, to make sure I wouldnt even open anything else to change unless you actually want to change it from where it currently is at. So put the new tire size in, then click done and load the customized files. PHP recommends you to not change anything at all unless necessary, such as tire size or gear ratio.
Like I said I am not an expert in these things, and anyone should feel free to correct me
but that is what I know from experience (I have 35" tires on my 2005 F-150), and from reading. also on a side note, to help answer the first question, you should let everyone know what truck you have and which modds you have done
, hope that helps!