It doesn't seem to make a huge amount of difference as long as you fit them in opposite directions. I used to always fit them with the pin facing down with the pedal to the front as it looked neater, the last time I fitted them the other way and have noticed a lot more play after a number of hard miles. I believe that this is due to the predominant (driving) force being on the thin end of the cotter so will revert to pedal-forward/pin-down in the future.
All the best,
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Julius Naim
London, UK
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