Nice pictures! The boron problem seems similar to the Rotala macrandra boron deficiency I had. It looks nearly identical. On mine though the deficiency became severe and almost all the leaves seemed to curl downwards along the edges. So the edge of the leaf tucked itself under the main part of the leaf. Calcium deficiency seems to look different, more like someone just pinched the leaf in certain places and the rest grows normally for a while and then pinches off in another direction.
Very interesting stuff. I'd love to see more boron deficiency pictures since it is very uncommon to see photographs of it in aquatic plants.
I think low boron levels might be the reason Rotala mac. is considered a hard plant to grow. I think it is much more sensitive to boron deficiency then most other plants and may actually require slightly more boron then is normally available in the water supply or CSM+B mix.
The holes are from snails chewing away at the leaves not other deficiencies.