Well as I suspected the pinion bearings were not in the master rebuild kit I bought from an Aussie supplier
http://www.ebay.com.au/itm/JEEP-TJ-W...UAAOSw7KJXEG1W
I noticed bits were missing when I first got it e.g. there was no shims, no bolts so I took a photograph and got sent those.
Confirmed on Friday night no pinion bearings so went and bought a set from Stateside bearings. Couldn't be bothered going back to the Ebay dealer and waiting for more bits to arrive, next time I'll stick with buying direct from the states.
Anyway whilst at the bearing shop picked up a huge hydraulic bearing puller kit (as one does).
So got the bearing off the pinion and the two off the pumpkin. Used the old ones to make up dummy bearings and set the pinion height. Tonight should see the rear pumpkin go in as I need to print out the pinion torque settings and preload torque.