I would suggest looking into powerline again. Junction boxes by their very definition imply wires behind it, in the wall. It really does sound like you want a wired connection without using existing power lines and without dropping new cable behind the wall. The only thing that leaves is inelegantly dropping cable in front of the wall, that would be through the floor and I really doubt you want to do that since you have a two story window wall. It's possible that with the layout of the house you could run the cable into a wall and send a drop of Ethernet cable downstairs along a different wall so that there's nothing affecting the large window area, but this is getting into aspects and particulars about your house's architecture that we just don't have information about.
Modern powerline has the ability to connect at 1.0Gbps, and can offer over 300Mbps of real throughput. That puts it well ahead of actual real-world WiFi and quite frankly, for an HTPC interfacing to a NAS, there is simply no media that can use anywhere near 300Mbps anyways. Even a direct copy of a BluRay rarely uses more than 40Mbps. I agree with you that using WiFi for this would be a bad choice, but then again I pretty much hate WiFi for anything except browsing. Maybe 802.11ac would be OK, particularly if you can setup a separate WiFi network on its own channel just for this. But realistically, powerline would be cheaper, more reliable, and more likely to get better throughput. All you have to ensure is that the outlets upstairs and downstairs connect in some way -- if your house has only one breaker box, then this is guaranteed.
(I would strongly discourage the use of crossover cables and second ethernet ports on other PCs though, as it forces the first machine to be on in order for the other to have any Internet access.)