Kyomu, for cycling, you might want to raise your saddle a bit. It sounds like it's too low which puts a lot of stress on the quads. When using a SPD type of pedal, a lot of power is generated with the hamstrings and not with the quads like normal flat pedals.
Select a small gear, aim for a cadence (crankset RPM) of around 100.
edit: for running you really want to get yourself a pair of proper running shoes, they have far better cushioning and roll than normal sneakers.