Araldite will do the job, its handy stuff. Others may have a better recommendations, but I see no problems with doing that.
Fortunately any changes will be nicely hidden by the plate I have TL with a Wilkinson I'm hoping to start fairly soonish. Have you increased the bridge pickup route? They are a bit small and slightly too far south in the kits, esp if you are using an after market pickup.
In regards to the nut, I think being slightly too wide is common, I've had that with some TUSQ nuts I've bought, nothing wrong with filing it down, so long as the string spacing is all good and neither of the 'E" strings is too close to the edge of the neck.