The best place to buy everything you need to build a bass is
www.stewmac.com, they dont have many pickups so you can get that on
www.bestbassgear.com, they also have a couple good preamps. For a neckthrough, the one thing that is easy to forget is the channel for both pickups, the neck pickup will be hard to reach unless you do a channel on your neck blank before gluing it up to the wings. For pups and Eq configuration, best thing I would recommend is to go around the music stores and try different instruments, take note of the ones you like the most and check out the specs on the manufacturers website. Otherwise pups and Eq configuration is really about what tone you like and others on TB wont necessarily agree, its all about opinions and in this case, only yours counts.
Its absolutely beautiful to read that you will build this with your grandfather, absolutely beautiful. Grandparents are great, they have incredible life experience. My grandpa passed away 3 years ago, I have a lot of his tools now, and the first bass I built was entirely with his tools. In fact the only electric tool was a drill press for the bridge and ferrules, other than that I used chisels, rasps, files, sandpaper and spokeshaves to do everything ! I dont regret this, I developed very good techniques with hand tools which proved indispensable on my other builds.
I wish you good luck on your project and hopefully this experience will be one to remember, a great time with your grandfather to remember ! Peace.