Well, while making them you need to make the foot part fit over a certain shor ot boot. Meaning if while you made it, you used a shoe base to make sure the foot portion even fit you, then unless any other shoe has the exact measurements of the one you used to make them, it will look bad. I think you need to start over and start by getting shoes or better, boots, that you will make these go on. And rain boots will be too wide in the calf just fyi. I'd use an ankle boot. I did that for 3 covers I made. That way you have full control over the measurements above the ankle. Then use those to build your covers around so that they fit.
This tutorial is what I used:
I made these:
The 3rd ones I don't have a pic of, but yea.
If I take those off and try to put them around, say, a riding boot instead of the ones they are on, they won't fit because the fabric is cut to match the shape and measurements of the ones they are on. See what I mean?