Have a look at the schematics from 1jz-gte.us - all this info is in them.
On the 26 pin connector:
Pin 14 is fuel pump control
Pin 16 is fuel pump speed control (which I assume you don't want to use).
Make sure you use a circuit opening relay (or something else with two coils). One coil is driven (pulled to ground) by pin 14, the other is driven whenever the starter motor is operating.
What is the donor motor from and what is it going into?