I think I have had similar pain in my feet. The pain on top is worst over the third to fifth metatarsals. When it's sore it hurts to the touch. At its worst I am unable to walk - each step feels like I'm walking on a broken foot. (I even went for xrays at one point).
It took me awhile but I eventually linked it to wearing less structured footwear (ballet flats, thin-soled athletic shoes, flip flops, etc.) I love walking but I have a terrible gait (overpronate, bunions, bad knees, tig7ht hip flexors/weak glutes) which I think puts extra pressure on my feet when I wear minimalist footwear.
Not sure if your situation is similar, but in case it is, my pain improved in the short term when I switched up my shoes. I found long term improvement from developing my foot strength and working on my flexor/glute imbalances.
Suspected SpA. HLA B27, xray, u/sound, blood tests all -ve. Ancient history of plantar fasciitis, SI joint pain, knee arthritis. Recent history of tendinitis, neck pain, debilitating finger pain and stiffness (especially mornings). No diagnosis, no meds.
2010 - stopped eating dairy
2012 - stopped eating wheat
2014 - stopped eating all grains
Jan 2017 - discovered NSD - 98% improvement in symptoms, continually amazed by my results, wish I'd found kickAS sooner