That pickup rout is very off indeed. However, if it can be covered by a correctly positioned pickup ring with the neck in position and you have enough wood underneath it to screw all four mounting screws in securely, then it should be OK. You''ll probably need to sand or Dremel off some of the wood so the pickup fits in when it's all squared up.

You'll be able to clamp it securely. I've just done the neck on my ES-3 and that's very similar construction. You will need good firm pressure, but don't overdo it as you can squeeze out too much glue and make the joint weaker, not stronger. However, given the rough nature of the neck pocket wood, I don't think that will be an issue here.