So after reading your thread, I've gotten curious about if this was actually possible. I've managed to figure out at least two ways to make a full energy cell frame, after a few hours of research.
I've gotten the idea from BevoLJ's tutorials. The tutorials are advertised on the applied energistics thread on minecraft forum: http://www.minecraftforum.net/topic/1625015-152-applied-energistics-rv-11-c-stacking-the-unstackable/. It is the third tutorial and about the 31:00 min mark.
The method is to use a ME interface and a ME encoded assembler pattern with all of the materials needed. So in your case, a pattern containing 40 redstone dust and an empty energy cell frame in the crafting grid, and a full energy cell frame in the output. Put that encoded assembler pattern into a ME interface and place a buildcraft transport pipe or an equivalent next to that interface. The interface will throw out the ingredients into the pipe. Then use some kind of sorting device, like a diamond transport pipe, to separate the ingredients into the magma crucible and the liquid transposer. Place either another ME interface, ME importer, or an equivalent to the liquid transposer and you should then get your full energy cell frame.
Another method is to use a ME exporter to constantly export redstone into the magma crucible. With this method, you only need to make an encoded assembler pattern with an empty energy cell frame as the input ingredient and a full energy cell frame as the output. You would then place that encoded assembler pattern into a ME interface, and that ME interface next to a liquid transposer. And the rest you should be able to figure out.
I do not know which method is a more efficient use of resources to create. Your problem was that you assumed that your applied energistics / ME network could read two assembler patterns at once. Applied energistics chooses only one assembler pattern route, so to speak, and sticks with it. In the end, you don't need more than one molecular assembly chamber, and these methods will work similar for the other things you are asking for.