I tour in shimano cycle sandels with capilene socks and neoprene overboots when it rained. keeps your feet supprisingly warm, dry unless it's heavey rain, and dries out really quickly even in a tent (unlike shoes which stay wet for ages). Strip off a layer for dry but cold and other for dry and warm.
If you are on a long chuff and it's raining, everything is going to get wet, even stuff in paniers unless you take extreme precautions. I use supposedly waterproof paniers then double wrap in plastic bags. That works most of the time.