So in my photo would you be saying that J2B and J3 are joined in the connector and still effectively running from the ignition switch to the coil and are still an active part of the start ignition circuit, with power coming from J1 via either R6 or A1A?
Looking at the coil it has 2 wires in to positive - the pinkish wire from the 4 pin resistor that I labelled Coil and another red wire, perhaps this is a continuation of J2B / J3? It's my only explaination, they disappear into a mess ofwires in electrical tape and the red wire comes out of it further along.
The black and yellow wire to the negative on the coil I think does run to the top pin on the ECU as shown in your diagram, there is a second wire (red) from the negative on the coil which I believe might have been to an aftermarket tachometer.