The best idea is to get a wiring diagram and connect things (like the fuel pump) up as they should be. Also it would help to know what model the engine came out of, and when you say body loom do you mean body loom of the donor car, or body loom of your car? ANd your car is a... ?
A lot of those wires you are asking about seem to be "custom" additions to the old loom.
1 - Yellow wire - Just a 12V feed to something. COuld have been anything, stereo, horn, neons, NA BOV speakers, etc
2 - Check wiring diagram
3 - Green wire. Check wiring diagram. Maybe additional tacho feed.
Trace through the circuit from ECU to ignitor to coil to dizzy and see what is stopping the spark. Every point should be getting power and a relevant signal (CRO is handy to check the signal, but hard to come by).
Also your alternator should have 2 connections to constant 12V. One from the main feed post, and one to the regulator, both are usually fat and white. Again check your wiring diagram.
Hen
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