Personally I wouldn't cut any wires from original bike harness. Is better to spend more money, but be able to go back to standard at any stage for example due to an qs issue. On the road you are always able to disconnect it and re-connect harness connectors as they were. But this is my personal opinion and no need to follow
First - those connectors are not cheapest and you won't be able to buy female plug from KTM dealer, as this is part of coil itself. You can buy from them only male connector, which is attached to harness. To prepare loom and avoid wires cutting you obviously need both parts.
Here is where you can get it from:
connector:
http://cordona.net/shop.htm#spareparts go right to the bottom of the page, the ones you need are third and fourth counting from bottom, both called "DUC 749-1198 M waterproof connector", male and female. This is the connector used by Beru.
When you get connectors, cut original plugs from the translogic qs and replace.
If you decide to go for it, I can tell you what wire needs to be cut and brought through qs to allow shifting to work and which ones must be just passed through. Hope this help a little.