you could have just put the knobs recessed and in the side of the guitar, so theyre not visible but still exist, might be kinda neat on a build sometime! youd hardly need knobs, just something to cover the knurl on the pots a little. could have a switch too... hmmm got my mind going now!
looking good, glad you got your neck problem figured out. looks like youre working fairly limited with tools, welcome to my world!
as for routing the pup first. just install the neck, and if its a little off, adjust the route a little to move it into place, and make your own pickup mounting ring the will hold it in the right spot and cover the route