After much reading and testing, I believe the easiest way to change tire size to ensure the trans shifts correctly and to satisfy the tune is to leave the tire size stock (ie revs/mile) and alter the gear ratio (under speedometer tab) to what would be the new effective gear ratio.
For example, a 3.73:1 geared truck with 37.5 "tall tires has an effective gear ratio of 3.18:1
There are many online calculators to help do the math.
Changing the revs/mile for the speedo, only corrects the speedo. It seems to do nothing for the trans.
After doing the gear ratio change last night, the trucks manners changed considerably. Very positive results.