Check with Kennedy for wiring questions on the controller, if it isn't OEM. If the controller is a simple 1985+, it should have Batt+ to one large pole, the other large pole goes to the GP's or GP harness, and Ign+ goes to the small "S" pole (just like on a starter solenoid). If it has a 4th pole, that is for the inhibit switch (coolant temp switch). Either way, confirm what you have with Kennedy.

You should never have to bleed the injectors if there is no air between the IP and injectors. Prevent this by removing the pink/power/front wire from the IP while messing with the fuel supply. Don't plug it back in until the rest of the system is bled. If you this, only minimal air will have to pass (most out the return), which will be negligible. The short route between the final filter and IP is only a small amount, but shouldn't have air in it unless you pushed air to the IP from the filter.