1) from my ignition barrel there is only two wires red (positive) black (negative) is this normal or should there be 4 (as this is what goes into the plug further down from the bike end)?
2) a previous owner must of broken one end of the plug as the two wires were just jammed into the half remaining plug. I thought I would do the right thing and cut the red and black before they go into the plug and connect properly (double checking with a test light they are both positive and negative) however now as soon as I turn the key the main fuse blows, so while I thought these other two wires (red with a black stripe and brown) were just surplus are they somehow needed and crossed wired in the plug somewhere and is this the cause of the main fuse blowing??????
If you look at the 09 WR450F schematic, there are four wires that go to the stock ON/OFF button. This is only because of the LED ON/OFF light. Two wires complete the circuit to the starter/ignition and the other two power the LED. If you have an aftermarket key, like the Baja Designs key switch, you only need two wires.
Sounds like you have a direct short to ground somewhere in the bikes electric circuit. But the problem really can't be in the key switch.
I would disconnect the battery completely and measure resistance to ground on the positive lead. If it goes to "zero" on the positive lead when you turn the key, then unplug the headlight, taillight, and anything else I could unplug until I got rid of the short. Then focus on what is causing the short.
If you don't know how to measure resistance, either learn how (its easy) or buy a bunch of fuses and just keep replacing them until it doesnt blow.