I know some regulators need the body grounded. Does your have a good ground. Usually at the point the reg/rec body touches the frame. Remove the reg/rec and clean off the paint to bare metal, remount reg/rec.
Went back to your pic of the reg/rec wiring and cap. wire positive wire from reg/rec goes to input of fuse block, so far so good. Another wire runs from input of fuse block to cap. The other wire off cap appears to run down into box to a switch? Not so good. This other wire from cap should go to ground.
If you look at the wiring diagrams posted after that pic you will see positive to one side of cap, other side to ground.
The way it's wired your reg/rec doesn't hook to the cap ground. Also in those diagrams the main fuse should not be placed between the cap and reg/rec. It should be between the reg/rec and cap and the rest of the system. The main fuse if blows should stop all power flow from the source of power, in this case the PMA and cap.
In a PMA/cap system the cap helps the reg/rec regulate the current flow. It does this by absorbing voltage spikes, smoothing the out put voltage.
In the first diagram, if the fuse blows the cap gets disconnected from the PMA, and the rest of the system, allowing the PMA to run poorly regulated. this can cause voltage spikes to over 20 volts. This blows bulbs and can damage other electrical items.
In the second diagram if the fuse blows it disconnects the PMA from the cap and the rest of the system. This is better as any unregulated output from the PMA can't reach the rest of the system. It can still bleed of power from the cap, that won't last long, seconds maybe.
Where the red wire going to the cap and from the reg/rec should be joined. A red wire from this joint to the main fuse, from fuse to switch is best. This completely separates the PMA and cap from the rest of system.
Some PMA reg/recs had just 5 wires, others used more, I think Honda did. Maybe Kawasaki too.
Fuses protect for too much current, not to much voltage.
Leo