Sorry to hear you had to stop. Better that than do yourself a longer-term injury though.
It seems, however, that you 'may' have provided me with the name of the condition that periodically afflicts me - i.e. Morton's Neuroma.
I first experienced it whilst downhill skiing - in a relatively short period of time of wearing skiing boots, I can start to feel what seems like coldness in my right foot only, affecting just the smaller three toes. I can wiggle my toes OK, and checking them it transpires that they aren't actually cold or overly compressed at all. It then quickly becomes a cramp-like feeling which, to be honest, is total agony. Occasionally there will be a twanging-type sensation, and sometimes the problem will ease away at that point. It seems now I always get it with ski boots on - luckily for me it usually passes, though not quickly.
I've occasionally had it hiking in leather walking boots as well. Never in 'normal' shoes, so I'd guess compression is the key is my case.
I'd always assumed it was the shape of the boot, even though my ski boots and insole were custom-shaped, and I could tell from the pain and the occasionally twanging that nerves and tendons were also in the mix. It never really occurred to me that the problem might actually be inside my foot: stupidly I guess I expect my right and left feet to behave the same.
Anyway, hope you see an improvement soon, and thanks for flagging this condition.