Hi Simon,

I had the same issue with my EXA-1 kit. I had to correct for it by sticking sandpaper to a flat piece of heavy MDF, marking the required angle on both sides of the neck heel and very gently tickling it back down to flat.
You've just got to be careful of your eventual neck break angle, and correct the heel accordingly to preserve something close to your ideal break angle.
I went too far on mine and had to laminate a shim on to the neck heel to correct so just measure and mark up well, and take it a little bit at a time and you should be okay.
It would also pay to check your scale length at this point and mark where the end of the heel sits in that front cavity when the scale length is bang on. They don't always sit hard up against the rear side of the pickup cavity.

I also found that I had to shave that extension down to get my chosen pickups to fit (EMG ZW set). if you are using the kit pups this may not be a problem for you, but if you are changing out, then it's something to hold in mind.

Look forward to seeing how you go, best of luck with it.