I wear neoprene shoe covers and big enough shoes that I can wear my thicker Smartwool socks. I found that my feet still got cold from stepping off the bike and the cold radiating up from the cleat. I fixed that by adding a thin insulating insole from a pair of water shoes. Big eough shoes to add insulation seems to be key.

For insulating layers on my body I prefer something with a light power-stretch fleece next to my skin. I seems to do a better job of keepiing the moisture away from my skin. I don't feel as damp and cold when I stop moving.