In our experience, a new, builder-constructed home (is that what you mean by custom-built?) is usually less expensive than an existing home in a nice neighborhood. We built our current home in 2000 and now couldn't afford to buy another home in our current neighborhood due to appreciation. We want to move closer to our church (NW side) but have been unable to find any existing home in a good neighborhood for less than we can build a new home. So we're building again.
We've been looking at existing homes for months but have found - at least on the NW side - a lot of issues with location. Nice homes next to scary neighborhoods, or with not-so-good schools, or in bad traffic areas. But homes in good, newer areas with good schools are out of our price range. (We're looking for 4-5 bedrooms.) We haven't even broken ground on our new home yet, but it's already appreciated $3000. (Same house in same neighborhood costs $3K more this month than last month.)
Now, the disadvantage is setting up a new house . . . things like blinds, paint, and landscaping. Tough to do that yourself with young kiddos. We're addressing those issues by: having our builder install all the blinds, using a builder that completely sods the front and back yards, and we're thinking of hiring someone to paint the inside of the house before we move in. However, our home situation is a little different that yours. We both work outside the home and have a 2 year old and new baby on the way, so our children will be less independent than yours - you may be able to do some of those things while your son entertains himself.
Hope this helps. Good luck to you!
K.