I experienced similar issues (and even had the same pedals and shoes, but that is irrelevant). My anatomy book helped me figure out the problem. The foot has three arches (or trusses) supporting the body’s weight, connected between the heal, the head of metatarsal I, and the head of metatarsal V. Metatarsal I takes more weight than metatarsal V, and metatarsal I is unique for having some extra shock absorption in its cartilage. The arches are flexible and provide shock absorption. Your SPD pedals and flexible shoes are interfering with the function of the arches, particularly the transverse arch between metatarsals I and V. If you want to use SPD pedals, you need a completely stiff shoe to ensure that metatarsals I and V bear your weight, without the pedal putting unexpected pressure on the inner metatarsals. It is hard to find stiff cycling shoes, particularly ones that ventilate and have enough room for your feet. But the running industry knows how to make shoes with big toe boxes that are properly ventilated. You can get zero-drop running shoes for like $100, and use them on a $50 mountain-bike flat pedal, and you will have a great setup. At least it is a temporary experiment worth performing to witness how great your feet will feel, so that you have something to compare against when trying out cycling shoes.