It could well be your stepper motor. They are 'fickle' things and can have this effect if they are not seating very well, or indeed if the motor is just shagged. The fact that the air bypass screw has been moved a long way would indicate that the stepper is open a fair bit ... what method did...

If this is the 'Brown' connector it should have the fuel pump relay power feed (white / purple) , starter solenoid (colour varies but often black), fuel pump power (from the relay .. white / purple) , RISTS relay feed (black / red) (no idea what this does .. I have never connected it!) , white...

If the fuel pump is priming on ignition turn the you must have most of it correct. The rpm input to the ECU is a bit of a 'run around' wire on a 4.2 Hotwire system. 1) You will probably have two wires bound in tape with small resistors on spade terminals .. the black / white wire from the coil...