Firstly, I want to say I am still using the version for MC 1.46 in the FtB Ultimate Pack, so this may no be relevant, but if you haven't made any changes besides updating it to work with MC 1.51, then this may still be relevant.
Since the compact focicium cell allows the generation of forcicium from raw energy, it should be possible to automate power-based FE production with any automation mod.
The problem here appears to be that no automation capable mods (Applied Energistics, RedPower, BuildCraft, GregTech, etc.) can access the cell charge slot from any side, all sides appear to connect to the forcicium slot.
If that were changed by, for instance putting the bottom side connected to the cell slot, automation would become possible.
If this has already been updated, carry on, but if not, it seems like the least code-intensive way of allowing power automation. That or allowing reverse-mode operation for the Converter like there is for transformers.
Any kind of automation would be better than doing it manually.
Also, what the heck does the button in the upper right corner on the extractor do? I can't find any documentation on it.