There is no way at all to automate Fluxed crystals. Not at all. It's materials for free. You might as well work for it a bit.
I do remember something about changing configs to allow you to use normal crafting grids to craft the things. But I haven't tried that yet.
You mean theres no way to FULLY automate fluxed crystals, you can automate the farming, and first stage of breaking the crystals with autonomous activators and you can automatically pull out of the cutter & refiner with steves factory manager. In the dev version of the mod apparently full automation should be possible, when we'll see that though I have no idea.
http://www.minecraftforum.net/forum...rystals-everything-changed-when-i?comment=100