The 4-speed is a very strong and durable box, and there is nothing wrong with it. It shifts well, but very refined combined with the 1HD-FTE; filling a synthetic ATF helps a bit. The response when pushing the accelerator is a bit delayed. The Engine and Gearbox ECUs are two separate units.
The 5-speed came with a new combined Gearbox ECU and Engine ECU, with a much better response. Also the programming of the IP is adjusted, and an adjustable turbo (for Europe). The 5-speed has LU in both 4th and 5th, and it has automatic engine braking (shifting down when downhill and holding the brakes partly on).
Other news were: Valve seat/face, intake restrictor with stepper motor instead of vacuum, improved EGR - with EGR cooler (EU), "straw" to suck oil from I/C, butterfly valves on the intake to increase intake flow speed on low power (EU), new instrument panel, and a terrible user-UNfriendly HVAC control panel.