Definitely worth filling out recruiting forms and sending an email to coaches at any schools of interest. While a 2 flat in general isn’t going to get much attention, the specifics—short training history, aerobically underdeveloped, decent 400 speed—might be intriguing to some coaches. So I’d make sure to include that in the email.
Others will have more nescac-specific knowledge but I suspect the threshold for strong interest at those schools is probably more in the 1:56 range. The threshold for Ivies is around 1:54, and the kids who get shut out of Ivies will often turn to these D3 options (as well as other strong athletes who want D3 in the first place). In terms of soft support, it’s going to vary by school, program, and year.
I think you’ll have a pretty good sense of things after sending those emails and, if he gets replies, chatting with the coaches. I would cast a wide net given the circumstance. You’ve listed some strong track programs that are getting inquiries from a lot of strong runners. Mixing in some weaker programs might help. Check out performance lists on tfrrs.org for results from current team members. You might also consider visiting a few campuses this summer and setting up a meeting with the coach. This can help an athlete stand out from the crowd, but also give you a better sense of whether a coach is interested in using her or his limited resources to help with admissions, if they’re hoping for a walk-on, or if they aren’t interested at all (the latter is unlikely given what you’ve described).
Having said all that, your son sounds like he has a bright future in the sport whether or not he is recruited. Runners like that can thrive at D3 schools.