You may want to consider doing all of your routing, drilling, etc. before painting your next project body.
Alot of times, I'll actually "mock" build my projects prior to paint so I can anticipate any drilling or routing that may need to be done ahead of time.
This would also apply to mounting the bridge and aligning the neck where it would require the use of clamps, etc.
The less you have to handle the body after painting, the less chance you have of screwing up your new finish.
As for the pickup ...
We still don't know what type of wood your body is, or what type of rig you'll be playing through.
You could eliminate having to route your body by looking into a "stacked" humbucker that would fit into that single coil route.
It may not be "accurate" in terms of replicating the EVH VH1, but it may save you alot of work and aggrivation.