I honestly feel like I should be awarded some sort of degree for the amount of time, effort and research I've put into coming up with this final 3. All 3 have their downsides, which I shall explain below. Bearing those in mind, which would you go for?
Nathaniel (really love the long form, but I feel it's a bit, well, long, and neither Nat nor Nate do it for me)
Elijah (the popularity bothers me as I want to try to avoid him being one of several in his class. It's a really nice name though)
Evan (not sure it goes as well with DS1's name (Jude) as the other two).
No idea about a middle name as I don't care as much about those - feel free to make suggestions with your preferred choice. Surname starts with a W, for initials purposes.