L, you've given your S a good foundation. He can work with it and probably do just fine. Although you may think a bit early to be jumping out of the "nest" at 16,I wasn't much different in age than he "moving" from a small school to one about the size he's now attending. Granted it was a bit of "culture shock" at the time, but I grew up fast and adapted and with the solid foundation S has, no doubt he'll do similar. So let it go as a "growth" time or "life lesson" episode for him and try not to fret.
He will figure it out on his own as long as you remain supportive (which you've been). Do not let your thought about him being away interfer in any manner with your relationship with your D. Allow youself some additional time with D, without smothering her, because of the absence of your S. Trickey balance but you'll do just fine.
As the years roll along we are eventually given the "20 - 20 hindsight" to look at the past and see how neatly the future has been packaged for us. That includes the given free will of others to do as they may along the way, including MLCers, and yet there comes the time when we realize we have been looked upon with a kind heart from elsewhere after all.
May you experience that soon. If not, be patient/