when i used to bike commute in boston, i used a fleece balaclava to deal with the cold/wet ear/neck issue. It was thin enough to fit under the helmet, but completely sealed off my head, neck and ears from the cold, wind, rain. Then, I wore a rain jacket (with thick wool sweater underneath if cold), rain pants and rubber duck shoes if raining or snowing. It was a fairly short commute-- around 6 miles, so no problems with the footwear.

if you don't have fender mounts on your bike, race blades work really well (they robustly rubber band onto the frame area). They are also very light.