Whilst I'd still be tempted to leave it a little longer before doing anything to the neck joint, you can obviously start to have a look and see if there's anything in particular stopping the neck fitting in fully. I'd rub some chalk on the pocket join area, push the neck in and the high spots should leave a mark on the sides of the heel. You can sand those down, repeat, sand repeat until it all fits nicely.
Not a great pre-wired harness you've got there. I'd be tempted to start again as the wiring lengths between the volume and tone pots are rather excessive and the wires will tend to flap about inside a bit. The pots with the green capacitors attached are the tone pots, the other two are the volume. The long bits of wire attached to the volume puts are the pot outputs which run off to the selector switch.
The red wire attached to the back of one of the tone pots is the ground wire for the bridge.
It's made slightly more confusing due to the factory wiring the pots in shielded cable, rather than the singles cores the wiring diagrams normally use. In some instances, you want to use the braid as a ground link, and sometimes it only needs to be connected to ground at one end.