Yeah 2006-2007 Box would be easiest regarding install. You wont have to hunt down a 3.9 rear diff, but you will have to get auto stubs to re-use your current front shafts. But then its going to cost more to buy.
You really should run a plated rear diff with a DCCD box too. which will further add to the cost.
3.9 R160 diffs are a pain to get your hands on. But if you are maybe planning to run R180 rear end, 3.9 R180 diffs are easy to get your hands on.
However if you ARE planning to run R180, 3.54 R180 is a pain to get your hands on, but 3.54 R160 is easy. LOL WTF!!!!
There is a 2006 AUD spec DCCD 6 speed box for sale on rexnet at the moment WITH the plated R180 diff for $5500. Not a bargain, but still a reasonable price.
You could buy that and for now run your standard rear diff until you get your hands on R180 shafts and hubs to complete the conversion.