Dead electrics.

Thanks Kawboy!  Sorry I missed your post earlier, I must have been typing at the same time you were. Ok that confirms there must be an issue with the ignition switch then, as I have virtually no power to the brown wire. I'm going to take it off in the hope it's fixable...

Ok I rebuilt the ignition switch and cleaned the terminals up. It didn't look too bad inside. I tested for continuity and it seems to operate ok in that respect.  I reconnected it to the bike but unfortunately it made no real difference. Only 1.2 volts coming back out of it. 
Just to see, I bridged the white wire directly to the Brown...Nothing happens .   Thankfully no smoke either.
Strange as I'm getting 12+ volts from the white wire.  Not sure what the next step should be?
 

A brief introduction to electric diagrams.
Switchs- On an electric diagram the switch pin connection shown is usually shown in normal operating position.
Usually, multi position switches have a notation somewhere on the electric diagram identifying the standard connections in each of the switch positions.
On the bottom of the electrical diagram for each of the KZ1300 wiring diagrams are the notations for the switch positions. I've copied the switch positions for the ignition switch and the main switch here for discussion.
 
 

I've found the issue... 

I re bridged the white wire from the multi connector before the ignition switch, which read 12.6 volts, directly to the Brown wire and noticed the voltage immediately dropped to 1.2 volts. Sneaky!
So I figured the white must have an issue. and followed it back to the main switch at the side panel. I removed the switch completely and bypassed it by plugging the 2 wires directly, and bingo, I have power again. So I guess it's a rebuild of the main switch as well.
That was a tricky one to diagnose!  Thanks again!

Your perseverance paid off ! 

Electrical issues and tracing- One has to realize that diagnosing electrical issues can be a pain in the ass. When using a continuity tester like a light with a wire and a clamp, that the power being looked for is only enough to power up the filament in the light. Similarly, when using a voltage meter, the power to indicate the voltage level is in the milliamp range. You can test a circuit and think you have power because the volt meter reads full voltage, but in fact you may not have power because the load of the voltage meter or test light isn't the same load as the operating circuit. The best that you can find with a continuity light or a volt meter for the most part is an open circuit.

So back to your initial report of "what happened"- you stated that in an attempt to tighten up the loose clamp on the brake lever, you managed to short something at the brake light switch and it sounded like a fuse blowing. I'll assume it sounded like a snap similar to a spark plug test. If in fact that was the sound, it was probably a bridge between the brown wire contact of the brake switch to ground, either on the brake lever body or the handle bar. That would be a significantly higher load than if your contact was between the 2 contacts of the switch and energizing a 20 watt light bulb. That brown wire feed circuit is protected by a 30 amp fuse, so before the fuse would blow to protect the wiring, the short would have had to exceed a 30 amp load for up to a second in time. It is possible that a brief short in a wiring system open circuited a bad connection of the wiring system and in fact acted like a fuse and open circuited the circuit.
Some of the more common issues that have popped up on the site are the wire connections to the fuse block and of course the connectors in the wiring circuit. Also when inspecting the connections and connectors also look at the crimped joints between the connectors and the wiring. Quite often, the resistance in a wiring circuit is not the mating surfaces of the connector but the connection between the connector and the wire(s).

You also noted that you have power to the rad fan so that tells me that the feed wire from the battery to the fuse block (white/red wire) has power to the 10A fuse for the fan but you may have a faulty connection at the fuse block between the white wire/red to the 30A fuse and not feeding full voltage to the 30 A fuse.
Anyway, right from the battery through to the output on the brown wire at the ignition switch should be a straight forward inspection. Look at every connection point as they are all out in the open. This particular portion of the electrics should be as simple to inspect as using your eyes and a flashlight. Forget the volt meter at this point. it's an open circuit. It should be as easy to find as a cut wire.