Ahhhh Grasshopper....when you can snatch this pebble from between my toes, you will be ready.

I've seen this before. my wife's foot used to go numb every time she ran. have you tried "SuperFeet" insoles, or having custom footbeds made?

Are the "pebbles" on the ball of the foot or the meaty part by the joints? Luckily my wife works for a reconstructive foot surgeon and has told me I have this too. I recently took up running again and had to try several pairs of shoes before finding the right ones. I did not have a problem until I tried some cheap RBKs and when the cushion collapsed I started getting the same problem you describe.
It is called a "Mortons Neuroma". Do a Google and read all about it. Basically "Mortons neuroma is essentially a nerve that has become enlarged" and that is why you are experiencing the numbness and pain.
Motrin will help along with a good cushioning shoe but to alleviate the "pebble" altogether your best bet is to go to a podiatrist that will give you an
injection in the area to shrink the neuroma. There are some other treatments too but your podiatrist can provide you with the best treatment.
Don't let him cut you open. This is not necessary. Just get the injection and you should get better. Remember, not all podiatrists are created equal so
one may be better than the other.