My issue is a little different - it's the laces of my running shoes, through the tongue, against the tendons of my ankle. I cushion them with the foam pads that came with a swimsuit bra.They're exactly the right shape and size. Might work for you too.
Mine are wearing out and I've googled bra pads. They're available online (these look similar, but I think thicker than the ones I've been using), but I'm thinking I/you might be able to get them at a sewing store or a swimwear store. The ones I have are just plain polyurethane foam. I don't think the ones with a fabric cover would work for running, but they might for cycling.



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They're exactly the right shape and size. Might work for you too. 
