After a little trial and little more error, I was able to get some decent soles on my clogs.
I used rug backing with about 1/2 a bottle of black paint mixed in, and made the templates from heavy duty cardboard - the sort used for book binding. This stuff is a pain in the (wherever) to cut, so i changed my original Dr. Martins type design for one with minimal turns and curves. I cut it with a dremel, and managed to keep all appendages.
Once cut, I gave the templates a few coats of triple thick varnish, to waterproof and make sure nothing sticks to em. This way I could be sure they were reusable. Tried to use low-tack glue to attatch them on the sole, but found binder clamps work better.
Once attached I filled the templates with backing and set them outside to dry. Some areas are a little thick, some are a little thin, it's a work in progress.
The sole on the right looks mushy because I took the template off too soon. I waited till it was fully dry and then cut the one on the left off with an exacto knife. I think it turned out pretty well.
I plan on making another pair with leather sew on outsolesole, and i am hoping that the flat surface will be easier to work with. And I can apply the backing while knitting the clog.