Suggestion also can be to begin the tournament as soon as the qualifiers are in the MD.. it means nothing to play with a qualifier if we don't know who is that..
The reason I started it early is to gain some popularity before the rush of thread on the first two days of the GS. If we wait for FQR to get over, this wouldn't be possible. If the thread keeps getting pushed to the second page early on, it would have been tough to get participation.
My suggestion as a participant in the development of this game type is make the first rounds have more than one set. The epic game I am preparing for "soon" will not allow the brusqueness of the first round to happen.
I like the chance of early surprise eliminations. Moreover, a GS game should get over before the GS does. So there is an additional time constraint which yours would not have. Also, many people would not be interested in many of the matches in the first few rounds here. This will effect your game too, but to a lesser extent. (In case you think I have revealed too much of your game, let me know and I will edit this post.)