In no particular order:
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Bike fit including saddle choice.
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Getting more fit off the bike to support those long rides. It is a long time to spend in that position.
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In general I don’t like leather shoes but if you have foot issues getting leather can make a huge difference because you can stretch it. I have wide Lakes and before ever riding in them the shoe stretchers were in there for a week to make room for my toes.
or
- Modern mtn bike flat pedals are awesome. I just put some on a road bike to help with knee issues. They haven’t let me down in any way. Wear shoes that are comfortable.