For about a month now, I have experienced a numbness on the top of my instep, about where you'd kick a football. I have had no injuries, nor was there a discernible moment after a jog where I felt any immediate pain. I am a 47 yr old, flat-footed, pronator and realize these things can start happening at my age, but the pain has been getting worse with rest, and last night, the pin prick pain to that area was severe enough to wake me up several times from my sleep.

I have tried every kind of different shoe I have, but the symptoms occur even while wearing house slippers. I have orthotic insoles for my flat feet, but those haven't helped either. Anyone experience something similar? My concern is less foot related and more kidney or diabetic precursors. I was kicked off my insurance plan and can't afford the outrageous deductible and higher premiums of Obamacare.

No you can't say that is pre diabetic, that isn't the way it happens. Does diabetes run in your family? It could be age related; it could also be related to a slight imbalance in your hip joints. It could be a circulation problem.

You see we can't diagnose on the Internet. Please see your doctor to get a proper determination.

Please view this excellent video.
http://www.youtube.com/watch?v=c7QewW3Up50
I have never seen a set of pictures that explained it as well.
Note the bones between the long bones and the ankle. (I have high arches and one of those bones actually protrudes upward on my feet, so when I dropped a door on one, it hurt for years.)
Note the deep peroneal nerve. A pinched nerve is often the source of both numbness and pain.
I'm not diagnosing, nor could anyone online. Just be an educated patient when you do see a doctor.
Meanwhile soak your foot in warm water at least twice a day, and gently rotate it. Wear slippers outdoors with waterproof soles.