It is tempting to look at the array of fuses in a car and think that the simple fusing arrangement in our old bikes could be vastly improved by similarly installing separate fuses for each separate circuit.
A car has a vast amount of wiring, most of which is hidden in very inaccessible places.
All of those locations are protected from the elements and experience negligible vibration.
The fuse board is usually in a dry location (normally under the bonnet or in the dashboard).
A motorcycle is a very different environment, in terms of exposure to moisture and vibration.
Each extra connection adds more vulnerability to both of those factors.
To use a sophisticated fuse system as an aid for diagnosis of an intermittent (or any other) electrical fault seems to me the wrong way round, not to mention the amount of effort.
First of all, how do you know that you have an intermittent fault? According to your post, the main (only) fuse blew once, but hasn’t blown again.
A fuse can fail as can any other electrical component, unless fuses keep blowing intermittently, it doesn’t necessarily mean anything.
Hopefully that fuse was of 15-20A continuous rating?
As you have pretty much made an SPG system, just complete it with the tail and horn grounds, AND a wire from the engine (from a head steady bolt maybe).
Then a single wire from the SPG to the battery
+ve (assuming +ve ground) with the main fuse in it.
This will protect from any direct short in the entire system, from runaway current from the battery
(this is the only source of runaway current), thus avoiding a fire/total loom meltdown.
The usually extremely brief period of high current won’t normally damage any of the wires in the harness, it’s more of a very brief pulse that doesn’t last long enough to seriously heat the wires.
I agree with TT that the generating system doesn’t need fusing, it is simply not capable of enough current to be a problem. This is where some others will disagree, fair dinkum.
If you do choose to install additional fuses, I think your idea of using the ground wires before the SPG is a good one. Right next to the SPG, I’d keep it simple, 1 headlamp area, 1 tail area, 1 ignition.
Food for thought, trace out the diagram I’d suggest.