This is one subject I know about

Pressure Regulator Control Solenoid Valve, guessing i just run a rising rate reg instead.
A: Why? It works.
Injector Duty Output for trip meter, guessing not needed as i dont have a trip meter
A: Yep..not needed
All check light wires, only needed for checking stuff/diagnostics?
A: Yep not needed
Vehicle Speed Sensor, now dont have a speed limiter?
A: Not quite. speed sensor is for overrun fuel cut and other emission related things.
Ambient Air Temp Sendor Input, hopefully not important
A: Air TEMP? That's for A/C unit maybe.
Auxiliary Air Control Valve, thats the one that ups the idle right...i can live without it i think
A: In a warm climate. Yes, you can remove all that stuff. But it's nice to have.
Boost Pressure Control Solenoid, only important for fuel pressure doover isnt it?
A: It raises the boost (and at the same time, the ECU switches maps) for high octane mode (not kidding).
A/C Relay, not running A/C anyway
A: Yes, that's for poofs and grandmas.
Variable Intake Butterfy Control Valve, already taken out of manifold
A: if it's removed..then you don't need the solenoid or wiring.
Neutral Position Switch, wont be needed with manual ECU im guessing
A: Auto to manual. Yeah. I'd drop it.
A/C ON Switch, once again no A/C
A: yep I'd drop it.
FICD solenoid valve, thats the think on the side of the manifold? can i just up the idle and live without it?
FICD is the A/C solenoid. Yep you can lose it.
only other things i need to know, with the 3 wire O2 sensor
A: the two wires with a resistance of 1 Ohm between them is the sensor heater. The remaining wire is the signal.
(on 4 wire 02 sensors, the 4th wire is signal shield/ground)
Blue and white, ones reference voltage and the other is the signal back to the ecu
A: talking alternator wires?
but what is the brown one? it was bunched up with 2 other IGN wires but i can see it needing more power....unless its got an internal heater or something
A: these modern cars run a lot of relays and minimal load on the ignition switch. Nothing like our beloved 1200.
and the start signal in the ECU, i just run the trigger wire from the key to it so that the ECU knows when im starting the car?
A: Yep. that tells the ECU to batch fire the injectors and advance the ignition to get the bastard started.