There's always a way, just depends on your skill level. It also depends on if you ever want to put it back or sell things. My initial thought would be to call Thunder-heart and see if they will sell you a new harness for their micro-controller. Then you can just use their wiring instructions and boom, done. It's been awhile since I looked at the schematic and would have to think about the best way.
Conceptually - From the high/low and the run/stop buttons the wires run down to the little grey box in the harness. That is the convertor, from there it goes to the micro controller high command input and the Kill command input. You can remove the convertor and replace with a jumper connector.
You can order the JST connectors and pins online (Wild Steed has them or you can search the internet). From the handlebars you have wires for the High/Low and a set for the run/stop. You can make a new jumper and cross the leads to where they should go.
Not sure this helps or not.
