My recent DNF at the 12 Hours of Mesa Verde has me digging for a long-term solution to my feet issues. This was certainly not the first time I have had foot pain in an endurance race but it was the first time that the pain got bad enough to stop me from pedaling.

After some research, it is pretty obvious that I am suffering from
Metatarsalgia, or what endurance cyclists refer to as "Hot Foot".
Precision Bikes has an article that perfectly describes what I am experiencing:
In cycling, it’s known as “hot foot” - a burning pain in the ball of the foot, perhaps radiating toward the toes. Severe cases feel like some sadistic demon is applying a blowtorch.
Hot foot occurs most often on long rides. It may develop sooner or more intensely on hilly courses because climbs cause greater pedaling pressure. The pain results when nerves are squeezed between the heads of each foot’s five long metatarsal bones. These heads are in the wide part of the foot (the “ball”) just behind the toes.
Feet always swell on long rides (more so in hot weather), causing pressure inside shoes that normally fit fine.
Hot foot is actually a misnomer. It’s not heat but rather pressure on nerves that causes the burning sensation. You’ll sometimes see riders squirting water on their pups in a vain attempt to put out the fire.So what are my options? Here are a few cycling-specific solutions I found:
1) Loosen the shoe straps across the toes
2) Use thinner insoles & socks
3) Re-focus the pressure. Many riders solve hot foot by moving their cleats to the rear by as much as 8 mm. Long-distance enthusiast may go back as far as the cleat slots allow. They might even drill new rearward holes. After using this remedy, lower your saddle by the same amount if you moved your cleats backward 2-4 mm. If more than 4 mm, lower the saddle about half the amount. So, if your cleats go back 1 cm, put the saddle down 5 mm.
4) Add metatarsal buttons. These foam domes are placed on insoles (or are built into them) just behind the ball of the foot. They spread the metatarsal bones so the nerves running between them aren’t pinched by pressure or swelling. You can find these products in the foot-care section of drug stores.

5) Purchase custom orthotics. These plastic footbeds are supplied by podiatrists or sports medicine clinics. Among their biomechanical benefits are built-in metatarsal buttons. Be certain the practitioner understands you're a cyclist, because orthotics for runners are not what you need. Cycling is a forefoot activity, not a heel-strike activity.

Since I already do what is recommended in #1 and #2, my plan is to try the simple forefoot pad with a metatarsal button (#4) to see if I get any relief from it. If it helps, I may pursue a custom orthodic with the metatarsal pad built into it.
eSoles offers a cycling-specific footbed that is low volume and has a metatarsal pad option.
As a last resort, I may slide my cleats all the way back but this goes against everything I have read about achieving a proper bike fit.