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They can access shift points and pressures in an auto. Also tune for tire diameter if you are running an aftermarket setup. Usually fan temps are lowered, but arguably it is not a good idea unless running a colder thermo. After a dyno tune, a good tuner will do further fine tuning on the street. Here they can do things like smooth the idle and decrease decel noises etc.
Even with a stock thermostat you should lower the fan operating temps. I did 200* off and 205* on for the low fan and 205* off and 210* on for the high fan. Works pretty good keeping the temps down from the 236* the high fan did kick on. If you're worried the fans will run too much then go 5* higher on each setting. I've usually got the AC on so the fans are on low anyways before even hitting 205*.
It looks like you have a FRC so;
CAGS eliminate?
Turn off the AIR codes so you could remove it?
Rear O2 delete possibly?
The tuner should know all this if he is any good.
Don't know what you have done to the car to know what would likely be tuned.
Ask that he go more than 170' on his roadtest to check for driveability issues like mine prob did.
Lots of stalling, garage shift (all temps) issues.
A4 3.42 non existant WOT shift points. Gotta back off to shift.
Many more that im too lazy to type now.
Best of luck to ya.
Dang, you really need to take it back! I had the same issues in my A4 w/ 3.42's after the install. My tuner was able to tune for the gears and tire diameter on the first shot before even getting in the car. Shifts perfect at the very beginning of red line every time now.