Your kid sounds a lot like mine, only academically a notch stronger. There’s a lot of overlap between your list and ours as well, and based on our experience I’d say (although I’m normally very cautious in this regard) that you can dial back the safeties. (Though step up expressed interest in your matches – I saw a lot of high stats kids rejected from Case and U Rochester.)
Also, has he considered Rice? I know it’s out of your geographic area, but sounds otherwise like a potentially great fit.
Here’s how I’d pare the list…
Reach: Amherst, Brown, Harvey Mudd, Pomona, Stanford, Swarthmore, U Chicago*, Williams
(Keep what appeals most, bearing in mind that Williams and possibly Amherst may be a bit preppy/sporty, and Mudd, Swat & Chicago pretty high on the intensity scale). Maybe add Rice.
High match: Bates, Carleton, Grinnell, Hamilton, Haverford, Middlebury, Tufts, Vassar, Wash U, Wesleyan
(I’d keep Carleton, Grinnell, Haverford & Wesleyan for sure unless you see show-stoppers of your own. Take a look at frat life at Wash U. Not sure about Tufts. My sense is that Bates, Hamilton, Middlebury and Vassar are more humanities than sciences, but I’m sure someone can second guess that. Bates is probably more match than high match.)
Match: Case Western, Oberlin, Rochester
(All great choices. I might bump Oberlin up to the high match category and ask around about music opportunities for non-conservatory kids.)
Low match: Dickinson, Earlham, Kalamazoo, Lawrence, Lewis and Clark, Occidental, Puget Sound, Skidmore, Willamette, Wooster, UIUC
(Most of these are probably safeties. I’d keep Kalamazoo, Lawrence and UIUC. Don’t know much about the others – other than that they’re generally well-regarded and generally offer good merit. We did visit Wooster, which we liked very much but which didn’t seem to have a very robust Physics department – though they’re big on mentored undergraduate research – and Skidmore, which was lovely but seemed more about the arts and humanities than the sciences.)