I used Meguiar's cleaner wax about a month ago, after washing and clay baring. Today I just used the quick detailer that came with the clay bar kit, after washing of course!
Meguiar's A1214 Cleaner Wax - Paste - 11 oz. https://www.amazon.com/dp/B0009IQX0E/ref=cm_sw_r_cp_api_6SmnzbV4JRVER
Mothers 07240 California Gold Clay Bar System https://www.amazon.com/dp/B0002U2V1Y/ref=cm_sw_r_cp_api_WTmnzb8AET2XB
OK, so here's where I'd start. Try Iron X on the spots on the body. They really look like industrial fallout, and being in Philly, you're in a prime location for it. When I lived in Detroit, I used to get this all the time. Here's a google image search example, which looks very similar to your photos. Also, Scoobies are known for soft paint so this kind of bonded mess isn't unheard of.
As far as the painted sections of the wheel wells are concerned, I'd try maybe a cleaner wax, or maybe hand polishing, which almost never works, but might given the softness of Subaru's paint.
Otherwise, I'd probably contact a pro in your area that is more familiar with the types of bonded contaminants you're seeing.