Sean,
Personally, I would find the 98-00 1uz VVT-I engine. You get the better head design and don't have to pay for the premium of the 3uz engine.
I think you need to consider future power output when selecting the engine also. 2uz is cast iron 2 bolt main while the 1uz and 3uz are aluminum block (with 6 bolt mains). So, you can either sleeve your 1uz for the larger bore, thus keeping the lighter block. Or stick with the 4.7l and upgrade the main caps in the 2uz.
Rods are weak in the 98 and newer motors, so plan on building one if you want any sort of power.
From looking at the blocks, I'm pretty sure all of the blocks are strong enough to run 1,000hp with the correct supporting mods. However, I'm not sure how many have proven this.
-Brad