How can I improve the texture of my whole grain pancakes?
Debbie's right about the gluten - overmixing is a reliable way to get tough pancakes.

I'm not sure what the best solution is within your process. By far the easiest thing would be simply to use wholegrain wheat flour, letting someone else do the grinding for you.

Failing that, I think you want to grind the grains up dry, and then it really won't take much mixing at all to eliminate clumps. That's going to require something other than a blender, though.