Some people are prone to compressions on the top of the foot.
If you lace up shoes too tightly, they will constrict the nerves that come down on the top of the foot and damage them.

I now use the alternate lacings recommended here:
http://www.fieggen.com/shoelace/lacingmethods.htm
Normally I link to NorthCoast footcare, but Google is putting up some warning when I try to go there today. Their lacing suggestions for compression of the top of the foot, involves skipping holes (only using every other one). I then use elastic laces to take further pressure off.

I'd think about different shoes also.. do you HAVE to wear those boots?

A visit to a good podiatrist and some xrays, and exam for mechanical issues in the foot may help you.
I can only wear lacing shoes with very soft padded tongues, and the alternate lacing style...loosely... or my toes go numb.

Pain in the ball of the foot can indicate damaged sesamoid bones.
When damaged they move and inflame the tendons there, causing a painful tendonitis.