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I`m not quite sure if it`s do-able. Besides the worry of a toggle handling the current going through an ignition switch, there is the configuration issue. Also one of your black wires should be the kill wire which is normally black and white.
On a normal ignition switch, in the off position the green ground and black/white kill are connected. In the on position the red positive feed and the black accessory are connected.
Depending on how the 3 prongs are configured would depend on how you could connect up the wires. You could attach the red feed on one terminal and the black accessory on another to give you a simple on/off switch, but then unless you have a separate kill switch there will be no way of stopping the engine.

Just noticed from the wiring diagram that if you`ve unplugged your kill switch then even when you turn the ignition switch off you won`t have a feed through the kill wire to the cdi. If you plug in the kill switch again, set it to run and put your jumper lead on. Start the engine then turn ignition to off to see if it cuts the engine. If not then press the kill switch to see if that cuts it out ?
Just wondering if this is some kind of earth to chassis/engine problem ?

Electrics are all black magic to me but here`s my two penneth.
At some point in your system an earth is crossing over to a positive wire when it`s not supposed to, either in a unit or by bare wires touching each other in the loom.
Bearing in mind that I`ve no idea if the wiring diagram in the service manual is identical to the wiring on your bike, but looking at the wiring diagram it seems that the battery positive feed goes via a thick red wire to the starter solenoid, then a thinner fused red wire (presumably spliced onto the thicker one), goes to the main fuse box assembly, through another fuse, then splits to two red wires. One goes to the regulator/rectifier, the other goes through a multiplug to another multiplug attached to the main speed/fuel/temp display on the dashboard.
It might help to try and isolate by disconnecting each of the components in turn (reg/rect, dashboard, starter solenoid) and switch on the ignition each time to see if the fuse still blows. This may help to isolate the problem to a certain unit or to a certain point in the loom.
As Cruiser mentioned, the black/white wire is the kill wire and will be showing an earth with the ignition and kill switch off. If the wire shows an earth with both ignition switch and kill switch in the run position then it might be wise to disconnect the kill switch to check if that is causing the fuse to blow.
Good luck

This is just a possibility, but maybe someone has tinkered with the engine before you got hold of it. Maybe they`ve put in the wrong crank or cam chain, realised their mistake when they went to rebuild the top end and just chucked it to one side ?
At this stage I`d be tempted to find another engine and worry about this one when you`ve got more time....or count the links on the chain and compare with the link count on a normal 139qmb chain

Hmmm very strange, I haven`t come across a 1/4" difference in crankcase measurements before.
Just to confirm, looking at the simplistic pic below, the top diagram is how things should be when viewed from the flywheel side.
The bottom diagram is how the camchain is in your engine ?

photo hosting

Cheers buddy

Yes you`ll suddenly start feeling some resistance when you pump the lever, and it`ll slowly get better. Sometimes you have to pump the lever almost in slow motion at first until you feel pressure, can sometimes take 15 minutes or more. Leave the bleed screw tight and the master cylinder cover off, you should be able to see little bubbles pop back up through the fluid in the master cylinder.
If that doesn`t work, pull the lever to about half way through its travel and put a cable tie around it and the handlebar grip, then leave for a few hours and it`ll probably self bleed back up through the cylinder.