If they are custom tunes then there isn't really any need to change stuff. Bill writes the tunes with better shifting for both regular driving as well as WOT. I can't be sure where he set your WOT points but raising them probably wouldn't be a good idea. I've noticed my rpms can spike at 5600-5700 which isn't very good for the torque converter.
The gear ratio and tire size will be set to whatever size you gave Bill on the order form so there also isn't a need to change them either.
For shift firmness, making it firmer could possible cause problems with joints and stuff after the tranny(including the transmission itself) while softening them too much can cause unnecissary wear on the tranny.
Bill's custom tunes are a quite a bit better than his canned tunes so I would leave the settings how he made them.
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