Unless you're Superman and can see electrons moving inside wires, there's absolutely ZERO way any human can just look at wires and determine its ability to conduct electricity. Luckily we have instruments that can... This is 5-minute fix with multimeter...
Note that EFI system is on completely different circuit than starter. You can remove entire EFI system: ECU, injectors, coils, sensors, fuel-pump and tank and all their wiring and bike will still happily crank all day long without starting. Just because it cranks, doesn't mean EFI system is OK. Lots of possible causes of this.
1. HISS not satisfied with key. When you turn key ON, HISS light should light up solid, then go out after 3-5sec. Does it do that?
If HISS light stays ON, ECU's not happy with ID from chip and it won't fire sparks or injectors.
Use original key that started bike when covers were off.
Take close look at key and make sure ID chip hasn't fallen out. Many aftermarket keys have this problem where ID chip isn't securely attached.
2. wiring problem. With key ON, start/stop=RUN,
measure voltage at ECU, injector and coil connectors. If there's no power, then you've got ign-switch, kill-switch, relay, fuse, sensors or wiring problem.
Sure way to verify ECU is to measure grounding-pulses on injector & coil trigger lines with oscilloscope. High most of time at battery-voltage with intermittent drops to zero when ECU fires coils & injectors.
3. IF ECU does send out grounding pulses, problem may be wiring downstream between ECU and injectors/coils
4. IF NOT, still may be problem upstream from ECU with ign-switch, kill-switch, relay, fuse, sensors or wiring problem
I say restore bike to previous state when it did run. Reverse your steps and remove bodywork in reverse order you installed them. You may have pinched & cut some wiring internally somewhere. Or disconnected a plug, etc.