G'Day all!
I just thought I had better share this as I have found it fixes the Rear Door Rattle that we have experienced with our JK since we got the larger tyres/wheel combination.
Basically, there appears to be 2 causes.
1. The origional Bump Stops don't touch the Spare with the difference offset wheel. Easy solution from quadratec
http://www.quadratec.com/products/16053_520.htm
2. After scratching their heads and saying "We can't find it" at the Dealership, I just took a spanner to the bolts holding the Spare Holder onto the rear door. Funnily enough, they were loose. Tightening alone significantly reduces the rattle.
So, basically, with the above 2 measures, it's pretty much eliminated!
Yay!