Looking great. Glad the glue held and all is well.

Six pairs of big magnets pulling on those strings - you might loose some sustain as a result, but it will look pretty awesome. As you will be lacquering the fingerboard, any black wood dye should be fine as it's going to be sealed in so you don't have to worry about getting dirty fingers, though others have used leather dyes before to good effect. You can often get them in a marker pen form, which would make it easier to 'draw' round the inlays to avoid staining them. It will simply polish off the frets.

If you are going with 3 pickups you need to start thinking about switching and control options as you'll need to drill the holes for them before you start the finishing work on the top. You can use a rotary selector switch (like on some PRSs) rather than a Fender style 5-way, or you could use individual on/off switches, or individual 3-way off/series/parallel switches, or separate on/off and series/parallel switches (like Brian May) or..or.. too many options! But you'll need to make a decision and commit sometime soon.