Leg/knee warmers, like arm warmers, are great for changing conditions. Those fall days when you can start out with frost on the ground and have it be 70°F by the time you pull in. When it's full cold and you'll expect to want to have your legs covered for the whole ride, tights are best.

I prefer tights with no chamois, for three reasons: (1) full legs can pull on the chamois so it moves around on my body and chafes, the way shorts don't; (2) tights worn over shorts with chamois mean that I can get away with wearing tights a few times between washings, so I only need one or two pairs of warm tights; and (3) I can wear the same tights for cycling or running.

+1 on the shoe covers. I've never been able to wear toe covers, they cut off my circulation and I wind up with colder feet than if I'd worn nothing over my shoes, but some people like them.

Just blocking the wind on top can make a huge difference, and you can wear your running base layer(s) under your jersey. I'm a huge fan of merino wool. I also like a wind-blocking jacket with zip-off sleeves - useful not only for changing conditions, but it's like two garments in one, for rides where you might want either a vest or a long-sleeved jacket for the whole ride.

Make sure that your gloves have grippers on the palms, and enough flexibility in the fingers that you can hold onto your bars and water bottles, shift and brake without interference.

+1 on shopping TE!