Sorry no one got back to you earlier - until recently, Tim used a Boss OC-2 Octave pedal. Now hes using this:
(I have no idea what that is).
In any case, you should be able to cop a similar tone by using the Octave Divider mode of the Pitch Shifter, bring up Lvl 1 (1st octave down) and set Lvl 2 (2nd octave down) to off. Adjust the Mix parameter to mix in the direct signal so that its louder than the 1 octave down signal. Tim almost always uses the effect with distortion, so if your going into a clean amp simulation I would attach a drive pedal after the Pitch. Definitely use the bridge pickup.
Sorry that I don't have my Ultra in front of me... I'd be able to give you more exact settings.
Hope that helps!