Thanks so much for the extra information. I really appreciate it.
I suspect he's got a little infection going on with that foot.
My suggestion is to call your regular vet in the morning and schedule an appointment for them to see your pup and see what they can determine. I would request that they do a skin scraping of the affected areas (where they use the edge of a scalpel blade to gently scrape off the top layer of skin, looking for any mites), and possibly run some blood work to see if there is a thyroid issue. They skin scraping will also determine whether it's a bacterial or yeast infection...my suspicion is that it's a yeast infection since you've mentioned the odor, and that's generally associated with a yeast infection.
Once the vet determines what kind of infection it is, they'll be able to get him on some medication to get it cleaned up.
In the mean time....I do suspect that this is a yeast infection, and there are a couple over-the-counter options you could try:
If that doesn't help, I've heard of people having really good success with several different 'home remedies' for yeasty paws:
*Tinactin or Absorbine Jr, both of which work on athlete's foot in humans. The Tinactin is generally easier to apply because it's a spray instead of a cream. Just make sure to not allow him to lick at the feet immediately after application.
*Soaking the paws in Epsom Salts will help with some dogs.
* Vicks Vaporub seems to give some dogs relief from the intense itch of the yeast infection, however since it sounds like it might be a little raw, you may want to skip this one, only because it can be painful on dogs with open areas (even microscopic...) on their skin.
*Washing the paws with Malaseb shampoo (available at your vet) twice a day.
I hope this helps!!