So with a bit of patience, half tube of Shoe Goo and over a tray of ice, I finally have a set of soles that look half decent (considering the mess they were in after my first attempt at clear soles using Shoe Goo).
They are still not perfect, but on their way to being wearable. I have also sealed the entire midsole in Shoe Goo and smoothed it with the ice to blend it in. Now the clear sole parts don't look like they are just glued on. They are setting up now and I will post more images tonight.
Last stage for these is splatter, but I still have not found the right colour for that.