Solder the wires to the DB9 connectors leaving the middle pin empty to make it easier to put the connectors in the body.

The order you solder the wires doesn't matter as long as the wires are matching on both sides.

After the wires are soldered, you can close the guitar and reverse the process of taking apart the controller.

Using a desoldering pump/sucker would be useful for any mistakes along the way.

Make sure to solder the neck wires to the male connector and the body wires to the female connector.

Fumes from soldering can be dangerous, so it's recommended to have a fume extractor next to you.