ah, an x99 classified board should have 5.1 support so 3.5mm for the z906 would work fine if you went that route
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1. you would need a receiver capable of outputting anywhere in the range of 20w to 100w per channel at 8ohm impedence. this would be listed on the spec sheet of the receiver. i would suggest in the 80-100w range to get the most use out of them although even lower powered receivers at 50w would be suitable. i've personally had good luck in the other room with a sony strdh540 we picked up for under $200 on a deep discount sale although onkyo are a good budget brand as well. other good brands (but often pricier) are denon, yamaha and pioneer (i use this on my main system). my own personal brand preference lies with pioneer. i would avoid "no name" brand receivers you might find like pyle (even refurbished name brands are better than pyle junk). generally a new receiver will cost you at least $200 on a good discount or at least $150 for a good refurbished.
2. i've not heard of a break in period for this set. while true that some speakers/headphones sound better after a break in period it is also true that many sound about the same after such a period. if you are worried about it you can calibrate them out of the box and then calibrate them again a few weeks later. while i do not own energies (i own the klipsch quintet iv [$500] and a klipsch sw-450 [$300] on my main setup and a pair of sony ssf-5000's [$200] in the other room) and have not noted much of a change over time from day one. as for whether there is a change it depends on the actual speakers being used as some do, some do not.
3. you have two options for hdmi. connect the hdmi out of your graphics card and send all signals into the receiver and then from the receivers output hdmi send that to your monitor (called video passthrough)... or if you dont like that idea you could just run a hdmi cable by itself to the receiver (and not use the receivers output hdmi) and it will show up as an aux monitor in your list but in reality only be used as an audio stream no video interface. it might also be possible to run hdmi out of your motherboard but so things play nice i'd use connectings out of your graphics card (unless you have no graphics card in which case on the motherboard is fine). personally what i do myself is hdmi out the gpu and then hdmi out the receiver to a tv.
4. that depends on how far of a distance you need them to travel. in general i would say 16 (thicker, better) or 18 (a bit thinner) gauge speaker wire is fine. if you can get 14awg for the same price then great. here is a nice chart - factor in your longest length of wire (including any up/down/sideways needs for running under floors, in walls, in the ceilings, etc). your load is 8ohm for the top portion of the chart
http://inwallspeakers1.com/wp-content/uploads/2014/05/speaker-wire-gauge-guide.png or if you are outside usa heres an awg to metric conversion
https://c2.staticflickr.com/2/1297/599107189_43882d2e6d.jpg i would also suggest (purely optional!) using banana clips on the back of your receiver (but using the normal binding posts on the back of your speakers) to make things a bit cleaner and easier to remove for cleaning. if you need to run through the walls i'd suggest speaker banana clip wall plates. you can see some of what i'm talking about in my own setup from my setup images http://postimg.org/gallery/ql0xj0nu/
5. sorry, cannot help you completely with speaker mounts for the energies and i've not dealt with them though i can tell you a few things. WALL MOUNTING: i will say that since energies are rear ported you do not want to flat mount them on the wall (with the keyhole tab) but instead want to give them some space and use the threaded insert for mounting purposes on a mount which is away from the wall. something like the omni-mount would work
http://ecx.images-amazon.com/images/I/41Xd2PDezQL._SY300_.jpg STAND MOUNTING: you can get away with many different styles of stand but i found this one had a review by a user specifically noting energy 5.1
http://www.amazon.com/Theater-Series-adjustable-speakers-satellite/dp/B0000CFYOL you have more options than what i've listed (search around a bit) but that gets you started.