This may sound silly, but where in the name of all that is shiny did you find EE3 for 1.6? the MC thread and what I can find of github (really need to figure that stuff out one day) says 1.5.2
In that thread and on that github. With the github, you would need to build it yourself.
Easier way is just go to the end of the EE3 thread, and look for builds other people are constantly doing. Every time Pahimar updates, they re-build it.
What you're seeing is that there is no official release for 1.6.x because it has never been ready for use. He just barely got DynEMC up and running ( and up until then all recipes were disabled. ), he has pretty much finished the calcinator, but the aludel needs a fair bit of work. It currently will not cook up items, none of the code is there ( last I checked a few days ago. ) Alchemical chests require items from the aludel. As I mentioned, Minium shards are not currently obtainable as he works to move it over to a new method of acquiring them. Divining rod doesn't do anything.
This post from Wliu ( post 5708 ) is the key one for ya:
http://www.minecraftforum.net/topic/1540010-equivalent-exchange-3-pre1h/page__st__5700#entry27966550
Getting the addon Equivalency is pretty nice btw. EE3 itself is still just geared for vanilla. Equivalency adds a bunch of copper, silver, etc. to the transmutations.
