My final bore design actually had no thermopiles or any other energy regeneration in it when I learned that every block that needs to be moved actually costs more energy, and the thermos produce less than they cost. Eventually all I build in the end was a big bore head (10x20) with a frame of deployers creating the 'tunnel' to stop lava from entering, and a combined catapillar/worm engine (mostly to make sure the 2nd tick only happened when the bore actually moved) and added the pipes for immediate processing of the ores.
In total this was just the bore head + deployers and an additional 20 blocks or so, and about 20 pre-filled batteries. This thing run for over 2 hours straight and created so many resources that I will probably never be able to use them up: almost 200 diamonds, over 2000 iron, and more red/blue dust than the chests could handle (had to thrash them eventually). Building that thing took about 5 hours, researching it about 2 weeks. The initial cost was about 300 iron and copper/tin for the frames as well as some stone and redstone for the logic.
And the best about it: if I ever run out of resources, I just build it again in probably much less time and hook up the pre-filled batteries again. Unlimited resources thanks to Redpower.