Your system seems decently balanced, and as you are finding out, few homes are "perfect" for listening rooms. Let us look at your questions:
1) As mentioned by several people, most notably Alan, the QS line is a preferred surround speaker. I would hazard a guess this could still be true, but directional M3's may be a close second. I make this comment because of the distance from the requried placements to the listening position and lack of wall structure on the outsides of the speakers. I wonder if anyone has simialr experience in placements with openings on the sides of a QS?
3) Speaker wire is the subject of much conjecture and debate. It can polish an already very good system, but dramatic improvements are seldom the norm. Find a dealer you can trust and possibly audtion a few competing brands.
2) True, your room may not be ideal, but let us examine the options:
a) - based on the comments, abandon HT/Audio plans and systems
b) - renovate the room with help of an Acoustical Design expert
c) - build a system based on quality advice, choices and equipment. Then adjust the system to provide the best performance it can in your existing room.
I think you can determine fairly quickly that C is your easiest and most desirable option - that is unless you have a renovation in mind!
One thing that jumps to mind would be the levels you would be expecting in terms of volume. With the sheer size of the room, the openness could require a more powerful amplifier. But this really would depend on the levels you like.
If it were my decision, I would build as you have planned, and tune the system as required.