Ok so I had a read up and it seems likely this thing will be similar to a canam, and most of those do feed power through a main fuse and then an ignition fuse to the coil and the ECU shorts the coil to earth and controls the spark by turning the earth on or off.. Hope that helps.

The fuel and the ignition could both have power to them and then be controlled by the ECU earthing them. Wires almost never break inside the loom. They break at/where they go into the terminals where they connect to things, or they wear through and short where they rub on the frame. If there is a break in a wire, it's going to be inside that wire's insulation and you probably won't find it by looking. You need a multimeter that can check ohms and use it to check the continuity of the wires from one end to the other. You really don't want to be going pulling the loom apart just for a look. I'd inspect the loom for shorts to earth, (which will be obvious by the worn through tape and insulation) and check for continuity from one end of each wire to the other. You need to bear in mind that the power to the coil could come straight from a fuse, then be earthed inside the ECU and controlled by the ECU to fire the spark. Or it could have the same setup except with the power coming from in the ECU. Or the coil might have an earth wire(or not, it might earth internally) and be sent a short pulse of power from the ECU to make it spark. If it's the last option then there will only be a short burst of power in the coil's circuit when the motor is turning over. You really need to know or figure out which system it is so you know which wire is meant to have power, and when it's meant to have power. If you tell me where you got the manual from I'll try and download it and see if I can figure it out with you.. And do you have a list of the possible trouble codes? Is there one for the coil ?