the redpower component is simply pumping cobblestone out of the chest in the right corner (bottom picture) using a filter and into the crucibles. and yes, it would work for netherrack, but you cannot automate it that easily
If you don't wanna bother with the chest > transpoer setup you could always hook it up to a relay. The relay acts like a chest for machines that put items into adjacent inverntoires, it has a 9 slot buffer, and will auto-output items as the machines need them without needing a redstone signal or blutricity. Looking at your setup it would give you room for another stack of the magma crucibles if you wanted them.
For boilers, if you don't mind diping into gregtech, you could make a forestry rubber tree farm and centrifuge the rubber wood. This would give you 4 methane cells per 16 wood plus some plant balls that you can macerate into dirt. The methane cells can be put through a liquid transposer and fed into a liquid boler for about half the fuel value of biofuel. With this setup it would take something like 5 centrifuges per four boilers, due to it producing 4 methane cells every 250 seconds and it lasting a bit over 50 seconds per cell. The other added bonuses are coal cells which can be put through the electric crafting table for carbon fiber and sticky resin that can be centrifuged for rubber and even more plantballs and compressed plant balls.
As for my base, I still sadly have a lot of setting up to do. After I get all my temporary stuff set up I plan on finding a nice spot to drop either a 5x5 or 7x7 chunk quarry. What I want to do is make sure I have clear ground to bedrock so I can more easily setup my underground floors that will help with shard farming. What I'll do is on the roof of each floor have it covered with crystal clusters to help restore the aura and then have self made veins of smooth stone that will get infused by the excess aura. On ground level I'll have my farming stuff (with any addition stacks of stuff like farms hidden underground) as well as a village surrounding the area for villagers to spawn in. In the center of the area will be some arcane levitators to get to my floating castle in the sky, which I plan to be a geometric nightmare from below. I basically plan on the floors, starting from the bottom, to be different shapes starting from a triangle up to a dodecahedron, with it slightly getting wider with each shape starting from about 1 chunk in size to about 7 chunks. At the top of my floating fortress I plan on having a sky garden that will hold my thaumcraft nodes and silverwood tree farm, and off of the tips of my dodecahedron there will be waterfalls to ground level that will fall into little fountains so they do spread everywhere and make a mess.
The only problem I forsee having is making all the geometric shapes, more specifically the penta, hepta, nona, and hendecagons, especially since I want them to have more of a star shape rather than a circular shape, which makes it even more of a nightmare ><
Here we go, a list of what they'll look kinda like
http://en.wikipedia.org/wiki/Star_polygon