It really does look lovely..
What diff are you planning? What gearbox?? What clutch?
You out of the comfort zone for both 4AG and 3SG with 250bhp, so I don't see the T50 gearbox or T-series diff taking it. The J160 will last a while, but not forever.
The J160 Altezza box is bulky, although we haven't tried to fit it to the KE70 yet & I expect some panelbeating will be needed. The shifter tower is tall and long, so cutting the tunnel ahead of the gearlever is expected.
There are a couple of adapter plates to put the J160 onto the 4AGZE, but simpler would be to leave it on a 3SGE. That would solve the clutch problem too. However that's a very tall motor, so you might run into fitment problems. Then again, the 4AGZE drops straight onto your crossmember, I'm pretty sure the 3S wont.
The 3SGE is all revs, nothing much happens until 4000rpm plus, so I expect the 4AG to be more realistic to daily. You should get more mid-range torque from a turbo 1.6L to overtake the 2L 3S, although the 3S will be easier to set up and tune. In the end it will be more daily than track car, so it needs to be pleasant to drive.
I dunno, there are pros and cons on both sides, you'll have to sharpen the focus on what you want the car to do and how much work each option will take. Talk to TRD KE70 about the rally car they built, they will know what gear you need like a clutch & diff to fit a 4AGE with a J160..