When I got my 5.13s installed I updated my Superchips to 5.13 (switched back to 87 from TOW as this seemed to be a better setting for me) as well. After a few weeks I noticed it was shifting too soon still....keeping the RPMs too low.... so I changed my gear setting in my Flashpaq to 4.88...just to see what it would do...and boomshakalaka.... the shifting improved....

Is it super dramatic...probably not...but I can feel a change it mine, (or maybe I just WANT to think I feel a change ) so you might want to play around with your gears on your Flashpaq as you might be able to get your 3.8 to run just a little bit better.

Might help...might not... but its free so no harm no foul... at least that was my thinking.

 

Considered this, but was worried about screwing something up between the computer doing one thing and what the actual mechanics of the JK are (5.13 gears with 4.88 computer setting)

 

I'm pretty sure the spedo pickup is on the wheels so tire size is all that should matter for that.

 

although now with the optional Superchips upgrade you can change your shift points............