Hi Argento and welcome.

It depends on which factory makes the kits whether these holes are drilled it appears. I’m currently working on a GTB and I also had to drill the ground wire and neck mounting holes in the body. On a JB-style bass the output jack should be in the control plate, so that should be no problem. It’s possible that the factory is dropping the ball on drilling these holes and this could be something Adam will need to look into.

For the neck mounting holes you need to make sure they are just big enough for the screws to pass through the body without gripping. So they will be a larger bit size than the holes actually in the neck.

The ground wire hole just needs to be long enough to pass the wire through, but you will need a fairly long bit to drill the distance.