I'm not too sure what's going on without seeing the car, but the easiest way to sort it will be to hook up a laptop and datalog while you run it through the suspect region. I'm assuming the smoke you describe is black? Also, did the car run through the same region of the rpm/press map when dynoed in third? What I'm getting at is that in third the car will build boost more rapidly than in 1st or 2nd due to the increased load. This can mean the engine may miss the tuned area of the map when in a lower gear. Do you have the autronic soft ware that allows for 3D viewing of the fuel and ignition maps?
What I'm guessing at this point (may be totally wrong mind you) is that the engine is running very rich in second where you describe because it is in an untuned area of the map. When tuning the 1FZ-FE in my crown a few weeks ago it was missing and blowing fuel smoke at WOT and about 5000. Initially I thought it was the rev limiter, but it was cured by leaning out the mixture. The feeling of ign cut was due to the spark breaking down in the overly rich compressed charge.
Also, grab a nissan 3 wire oxy sensor or similar and hook it up to the autronic and put it in the turbo dump-that wil also help diagnose probs-it's not a substitute for a wideband sensor but is still hepful.