@John Conklin Others can jump in here as they please, but my first thoughts... Diagnosis of a neuroma typically is shown on imaging, but in the clinic is easy enough to find as it's very localized and reproducible pain that can be palpated typically inbetween the bones of the foot. Aka, I push on this pea sized lump and you have blinding pain, but I can press and do other things in the region without any issue. Those are tricky and offloading the area with a donut pad can be a good first step - barefoot probably would worsen it though in my opinion. Metatarsalgia is a generalist diagnosis of "your toes are inflammed," which is kind of obvious but not very specific. The trend of stiffness/pain that dissapates with exercise but then becomes painful once a certain threshold has been crossed is a common presentation of many joint/connective tissue type issues. It seems your issue is very much pressure sensitive. Biking in your cycle cleats places more pressure into the forefoot, similar to loading on a calf raise, as well as the late stance cycle of running. Around the time that this became very painful had you dramatically increased your mileage? Or as a counter, had you had time away from running and then rapidly returned to it at previous mileages without a ramp up period?