Haven't started yet, but I'm reviewing the instructions from the kit (the full one with fretted neck) an I saw the neck gets a relief cutout for the box lid. But....the box I got does not have a recessed lid. That means I skip that step, right? I will prolly be adding a pickup, but at that point I'm just cutting a dado and re-enforcing the neck under the cut, right?
I haven't used the kit, you'll want to think about the fit and how much clearance you'll have for your fretboard. Remember that the action (the distance between the strings and the frets) becomes quite important, so consider that geometry. Will your fretboard lay so that it's surface is above the cigar box's lid? Think about where it'd be if the lid WAS inset, then where it's going to be based on your box. THink about how that's going to affect the geometry of your bridge based on its height relevant to your nut. Adjust as necessary.
Adjust as necessary is kind of THE advice when it comes to CBGs. I do apologize if that's not helpful.