It's really a personal working preference and your method of finishing the guitar. if you have the space to work on the guitar with the neck attached, then my preference would normally be to glue the neck on quite early, so that you can then fill any neck join cracks and finish the guitar as a whole. But if you are short of space, (and moving a complete guitar around with a wet finish can be awkward), then do neck and body separately, then glue the neck on and then deal with any neck join gap finish issues.

I'd leave the guitar to settle for a few days before deciding if there are any neck fit issues that need dealing with.

As the kit is fully hollow, you should have less overall problems fitting the wiring harness as it can go in via a pickup hole, which is a lot easier than trying to fit it via an F-hole. But the controls are a lot more spread-out than on a 335, so the harness will be a lot larger. Definitely easier to use latex tubing over pots and switches to pull them through the holes than using string or cotton.

As the wiring runs are quite long, and you can't shield the inside of the body, I'd also be thinking of using braided screen single-core cable rather than single-core PVC insulated wire or vintage push-back wire to minimise noise pick-up.