At this point, I would focus almost entirely on the athletic recruiting. Right now there are too many variables to nail anything else down. You will know about the athletic choices before senior year, which is plenty of time to then take that variable and put it into the merit and major mix.
Since at this point you would know if he were a top D1 recruit, I would cast a very wide net, reaching out to something like 50-75 schools, and focusing mostly on D3 with some lower level D1s in the mix. Once the dust settles and the list is narrowed, your son can decide which, if any, schools are appealing. If none are that’s fine, he applies without the soccer hook.
There are top academic d3 schools with engineering that give merit aid (eg Case Western, University of Rochester). But I wouldn’t limit yourself to those – your son’s interests may change and evolve, and, for example, a LAC without engineering might end up being the best option – so don’t limit yourself now.