I'll do my best to help with the limited information given.
This harness connects to the throttle switch and the EGR solenoid. The pins on the solenoid look bent, so you'll need to straighten them. The ground wire for the throttle switch goes to one of the bolts on the bracket.
These two wires go to the coil. Red to +, black to -. They're for the Pertonix electronic ignition.
I'm fairly sure that the brown and black wires connect to the thermal timer. Check continuity between the brown wire and the brown wire connected to the cold start valve. Do the same for the black wires. If they have continuity, connect them to the thermal timer. Black wire to terminal W, brown wire to terminal G. The letters are cast into the plastic on the thermal timer. You'll need an insulator and the correct terminals which I can provide.
This thing is an insulator that holds the main battery junction to the inner fender. Be careful, the top piece breaks easily and is NLA. If it breaks and the junction touches something grounded, sparks will fly.
The wires from the voltage regulator go to the alternator. Black to one of the alternator case studs, green to the field connector on the brushes and red to the D+64 terminal.
This is the reverse light and seat belt reminder switch. It screw into the side of the M40/41 transmission top cover.
That is the barb for the booster. You have the booster connected to the ported fitting for the breather cap hose.
I'll need more info to help with the other wires.