Well, since you're asking. Before you commit to a case, you might consider something to intake (1) 120mm fan (spinning slow). From the bottom of the case. This way you aren't recirculating hot exhausted air because heat rises and you are no where near the exhaust from the PSU. Cheap ones with a 3 position switch are fine although a 4 pin to a motherboard header could be speedfan controlled if you prefer. The case you've chose is for 80mm fan(s). They will be noisy and spinning them slow probably won't move sufficient air imo. Take in to consideration the airflow eddy that might be introduced by those fans disturbing an OEM CPU fan that distributes air around surrounding components like Northbridge, Southbridge, RAM, etc. that would normally be 'blown'.
To exhaust the airflow, just use your PSU. You want it to have a 120mm fan also. It will already be thermal controlled and spinning slow enough you don't hear it. I suggest a Corsair modular cable 500w bronze with the pinout for the GPU power. A Nocturnal CPU cooler would be nice but they are really only efficient in stand up cases because they are tall. Afaik
, they don't make a good low profile one for sideways (HTPC) cases. I use the OEM fan. I control it with speedfan and a custom tapered curve but there are alternatives like a water cooler with a good sized radiator which again, you'd use another 120mm or 2, spinning slow to dissipate its exhausted heat. This too would need to be coordinated with the case. I think the (2) 80mm on the case you picked would work but if I had a choice and was starting from scratch I'd research 120mm fans and a case hole to exhaust them/it.
The GTX1060 6GB is a good choice. Rip speed fps should be decent for encodes you may create and the vram is high enough to accommodate decent madVR algo's. You may want to use something less expensive like the 1050Ti ($139 at Frys) I suggested, to get you by until NVidia new lineup is released. That will probably be in a couple months. Then if you want to build a new HTPC, you will have a selection of a newer card to compliment it and you can resell the 1050Ti. The Volta is expected early 2018.
I would get a DeUHD compatible ROM drive. This way, if you want to rip on your HTPC you'll be set and chances are (if) more UHD ripping software becomes available, the same drive will probably work with them. Oh I see you're going to use DeUHD. See their list of ROM's.
I agree with bryansj. That's a lot of CPU for an HTPC but if it's pulling double duty for intensive use I understand. The i9 is starting to appear fwiw. I doubt either will help guarantee future proofing any more than say an i5 HTPC wise.
Be aware, HDMI 2.1 is coming....