... the spds put a lot of pressure on the balls of you feet...
I have experienced this problem, but it was due to shoe problems. In my case, the plate on the inside of the shoes had bent so that the edges stuck up. This made a bump that pressed on my foot. Note that there is an area in the middle of your foot where a lot of nerves go through a concentrated area, and pressure will give you numbness.
What I did:
1. Removed the cleats and plate, flattened the plate and reinstalled
2. Cut a hole in the insole so that there is no pressure on the middle of the foot (like a cutout in a saddle)
3. Check the shoe once or twice a year to make sure the plate hasn't bent again
Even if your shoes do not have a plate on the inside, you may want to cut the hole in the insoles to prevent problems.
I've had for many years and still do have numbness problems using SPD pedals. It's gotten so bad that the numbness now only goes away after being off the bike for a few days in a row. I couple years ago I came across an article about fixing this problem by moving the cleat so that the pressure would be more behind the ball of your foot. This has helped a lot but not completely.
Personally I think the problem comes from the softness of the sole of the shoe. Mt. bike shoes are not anywhere near as stiff as road bike shoes so the pressure from the pedal will always be there to an extent.
I use to use Look pedals and the rock hard soles of rode bike shoes and never had any problem with numbness. The reasons I switched was due to my foot slipping out from under me when starting out up hill at a street light among traffic causing me to swerve all over the place. Not to mentioned slamming my privates down on the top tube when this would happen. This happened to many times. SPD shoes and pedals just made life much easier except for the numbness. And being able to walk normal is a bonus.
I'm thinking two things:
first is: have you tried adjusting them?
Second is: have you tried different shoes?
I've always said that wearing my spd cycling shoes is a bit like walking around on my own personal concrete floor... On the bike, it gives you a surface to press your feet against, when walking though, it's similar to walking barefoot on concrete... The upshot is, it shouldn't be any different to your foot... You shouldn't experience any flex in the sole of the shoe...no single point contact... No hot spots... The shoe IS a platform. There might be issues with the contouring INSIDE the shoe though
The other point is adjustment. If you loosen the cleats, they slide back and forth so you can position them exactly where you need them to be for the most power transmission, and for a comfortable angle...I can envision if this were not adjusted properly it would change how your foot pivots as you pedal and might amplify repetitive stress.
Either way, a visit to a doctor might be good, maybe can tell you which one it is, maybe it's the foot equivalent of carpel tunnel, or it might turn out to be important for things in life outside of cycling.
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