I have s set of toe covers that I use in the winter over cycling shoes. They look dorky, but do a pretty good job of keeping wind at bay. The strap on the back can sometimes ride up above my shoe onto my achilles tendon, but not all that often. I can't say they keep me toasty warm, but they don't hurt. Mine are old Sidetrak brand ones made of heavy neoprene, similar ones are available out there.
Unfortunately you just have to try variations of them until you find a setup that does it for you.