Congrats on your success!
In the near future page 14 of the manual will include the following new paragraph.
" If this is your first programming session with canned or custom calibrations, choose NO to bypass this option to insure that custom files are built from valid data in the PCM. Simply opening the Custom Options menu in the first programming session may cause invalid data to be placed in custom files."
So drive the truck around for approx 100 miles then proceed with the tire and gear sizes.
Once again thanx for your keen eye to correct some things that were overlooked.
Enjoy!