I am looking at fitting 4.11 diff gears in my stock 97 XH Ute. It's a 5 litre with a 4 speed auto. I have been told this will mess with way the auto shifts. Is it possible to just manually shift the box. I only need it to run down the drags for one meeting.
Dose the Auto change gears form the speed of the car or the revs of the engine?

It will if you don't change the drive gear on the speedo transducer. You may not get a gear with enough teeth to work with 4.11's anyway, I think a 23T is the largest you can get and it may not be enough fpr 4.11's.
If you can't get one you can use a pulse adjuster kit from Jaycar and modifiy the signal.