Re: Who to fill a pup route and touch up paint job?
There's your answer right there. I mean, if you look at an older guitar you can see the split line where the body joins together. That's not only the same wood type, but sometimes it's a flip or bookmatched piece. The fill will show eventually. The best way to hide it is with an ultra high quality sealer/basecoat like the one Patrick uses. But that's more suited for a total refin.
My absolute answer here would be to first fill the single coil route with a well cut piece of Basswood. Next, route your humbucker. Now, route a shallow "swimming pool" route, about 1/2" deep from the outside edge of the neck humbucker route to the bridge humbucker route. No you have new wood going across the entire mid section. Over time, your tell lines will only show between the humbucker mounting rings, going in the direction of the strings. They will also kind of look like body joint lines. Whenever possible you only want to fill in the direction of the grain, and have your fills terminate somewhere hidden. That's my opinion.
Also I thought your title said "How to fill" not "Who to fill" thus my bloated rant. My appologies, but maybe it helps.