That transistor is for the 5v reference voltage for the Vane position sensor in the turbo. If the water pump had been replace check the wiring behind the water pump. I had seem a couple of Hilux were the 5 volts reference voltage was shorting out after a water pump replacement blowing the same transistor. The transistor I used is a PNP 60v 5amps Part No. STD888T4. I bought them from Element 14 in Guilford, Sydney under Part No. 108-4555. A new module was over 700 dolares from Toyota. The transistor is only a couple of dolars.
