Ceiling fan install fail! I have 12 wires in 6 different colors. Please help!
The "dark gray"s are actually blacks.   Gray is also a color used in wiring, and it has a very different meaning from black.  Yours is not that. 

Note that the wires aren't just random, they are grouped in cables entering the box.  

Locate the cable with a red wire.  Note that it also has a white and black.   This is the run down to the switch.  Cap each of these wires individually with orange or yellow wire nuts, tape the nuts down so they don't easily fall off, and pull the wires out of the way.  You will not be using them today. 

What remains should be 2 black and 2 white. One white/black pair comes from supply.  The other goes to your downline loads like the furnace.  Nut the black to the black, and white to the white.  

Turn the power back on.  Everything else should work now. 

Then call in a professional for the finish... or school up by getting a book on household electrical at the library, and reading most of it.  Not skimming or cherry picking.  Reading.