NA->TT Swap with the 5spd Transmission

Parts List:

2JZ-GTE, USDM complete with manifolds, accessories, turbos, etc
ECU for 6spd
Radiator
Igniter
Fuel pump ECU (Optional, but recommended)
Fuel pump with base and filter
Mass air flow sensor
Injectors resistor pack
Intercooler and piping
Power steering reservoir
Cruise control cable
Throttle cable
Fan shroud (just the big one, the lower one is the same)
TT Tach (good time for the TRD 10k RPM tach!)
Upper radiator hose
Heater hoses (3)
Clutch
Harness connector #10841 (to NA fuse box)
Harness connector #????? (to W58 transmission)

Required Parts for California Smog:

Air filter box
Intake pipe to turbos
Charcoal canister
Pre-cat and main cat
EGR assembly
Rear O2 sensor

Recommended Parts for Maintenance:

Full engine gasket set
Spark plugs
Vent hoses between valve covers
Coil pack connector clips
Other connector clips
PCV
Accessory belt
Silicone vacuum hose kit
Thermostat, gasket
Water pump
Timing belt, etc.
Lower radiator hose
Flywheel bolts
Pilot bearing
Release (TO) bearing

Tips:

Follow the factory manual on how to pull the NA engine
I kept the 5spd transmission but still pulled it with the engine. It's easier that way. In this case, drain the transmission oil too, unless you can somehow keep it from spilling out from the back. You will need the NA flywheel and clutch to use the W58.
The connector on the TT 6spd harness for the reverse light signal on the transmission does not match the connector on the W58 5spd transmission. Either buy a new clip or carefully remove the one on the NA harness and install it on the TT harness.
Keep the A/C compresor connected to the lines and in the engine bay. It'll bolt right up to the TT block.
You can keep the NA power steering pump if you don't want to disconnect the high pressure lines. You'll need to remove the NA reservoir and install the nipple from a TT pump that connects to the external TT reservoir. It'll be a good time to install a new O-ring at this point (mine leaked).
If this is a California car, the chassis will already be equipped with a rear O₂ sensor by the main cat. The NA sensor will work with the TT ECU and cat. I'm not sre what people with non-California cars do about the rear sensor.
Check all electrical connector clips for brittlenes, particularly the ones by the intake manifold. Replace where necessary.
Clean the injectors prior to installing the engine.
Follow the factory manual on how to install the TT engine
The TT has a separate fuse for the fuel pump (EFI2). Because of this, the TT harness does not perfectly match up to the NA fuse box. There are two electrical plugs, one matches, the other doesn't. What I did was replace the connector on the TT harness to plug into the NA fuse box. There are three wires on the NA side and four wires on the TT side. Three of the four wires correspond perfectly to the NA fuse box. I crimped the leftover thin black-red wire with the thicker black-red wire. I also used those wires as the signal to for the fuel pump relay. The dotted-line boxes in the diagram shows what I had to add or modify: