Yea it will be a little more money to go NA-T on this motor but on the long run you will be making more power. The 1JZ makes a little bit of more power than the regular NA motor, not to mention the wiring fun you are going to have

. Going ot look nice definately when its finished, first 1JZ SC300 I'll see in person.
I tried coming by your shop yesterday but you looked busy and I was in a hurry to get to Tampa Bay Auto Sounds so they can look at my alarm since its acting funny. I'd definately like to check out the ride sometime. How much did the TT brakes run you?
As for for the throttle body running over the head on the 2JZ-GE - They make 2JZ-GTE-like intake manifolds for these motors, I can get them for about 500 and the stock TB still fits on it perfect.
Dyno run with that intake manifold on an NA-T:
Check out the NA-T site... you will find it useful:
http://speedtoys.com/~daveh/93na-t/