Hi all. I'm really like thorium, and automatisation. And i like small count of reactors (because of automatisation) and big counts of EU (because...never mind). So i'm using this one if i have no a lot of copper input, this, if i have copper (or this to get more EU at a time) or this, if i have recourses for it.
I can't imagine how to improve efficiency of it without reduction of power output. And i think, it's can be a way for it.
take a look at my thorium based "portapack" design. try that, it produces 1/3 the power of yours, but is only 1 block, so stick down a couple lines of them (redstone in bottom, fuel in side, power out top, spent fuel out other side) you can fill the empty slots with reactor plates or something. That would be easy to automate, and will produce a higher power density than your current system.
Simlarly, you could use my 70EU/t single block plutonium design.