Hi Mateyboy, your plans sound good. So is the EX body you have routed is the neck pocket the same as the kit ? Assuming it will be a set neck you need to insert the neck into position and mark a line where it meets the body. You need to mask the neck heel where it will be glued and it has to be masked for the whole paint/clear process.
Might help to post a pic of the neck in position and be good to see the body you routed