First Build SMS-7Q

Hello everyone! This 7 string will be my first build. Everything looks pretty good coming out of the box. So far the only issue I have run into is the routing for the neck pick up seems like its 1mm to high. With the neck inserted completely, there's just barely not enough room for the neck pickup to slide in. I could remove some material below the neck pick up until it fits, but I think if I do it wont look as clean as a perfectly straight routed line. I could definitely put a 1mm shim inside the neck slot and that would open up just enough space for the pickup without removing material. The only thing I THINK this would change is the scale length, and I think once I adjust the saddles it would compensate for the change. I'm hesitant to mess with the neck and where it sets into the body at all, so any advice is going to be greatly appreciated.