The only inherent problem that I see with the 3T GTE is that they use a bit of oil (any engine will when revved repeatedly and 20+ psi will help you use some more) and that you can well do with larger sump.
I would hestitate to just get into a 4A GE and turbo it as there is quite a bit of work to turbo an engine that wasn't fitted with one originally.
Brakes - you mention slotted and drilled; but what are they off? Are they bigger than standard?
I have 10.25in rotors on front with 4 spot HiLux calipers + I went disc brakes rear.
I must warn - fitting this engine to the KE20 is not for the feint hearted - it takes a lot of work and patience (if not downright stubborness) in my experience.