EDIT: Marc beat me to it as I was typing, but here is my answer below:
I used a LHG cuben solo w/ awning on a thru-hike. Its slightly different than the So-Long, but similar in the basics. I set it up virtually every night and I loved it. It did however take me a while to learn to get a proper pitch, which I think is pretty typical of most non-freestanding shelters. Each design has its own character and ultimately practice makes perfect.
Most of my early problems boiled down to getting the tent "squared" with the placement of the first stakes before anything went up. (BTW just to be certain we are on the same page, you have to stake out the tent body before you place the poles or touch the fly.) I would guess "Squaring" is very likely the beginning of your issue with getting a tight pitch. Properly pitched you can drop that awning pole in the middle of the night, and go right into storm-mode set-up tight as a drum.
For #1 you have 2 options: Storm mode or awning mode. In awning mode you need the awning pole or a properly sized stick to get the pitch tight. In storm mode you need to connect the three fairly close tie-outs on the awning together; no stick required. Your picture shows awning mode with no pole. Connect those three tie outs with a small carabiner and your good to go. (That is what those tie outs are there for ... I cannot tell if you added guy-lines but only the center one on the awning needs it.)
Not certain what you mean on #2, but for #3 you just need to balance the length of your poles ... in your picture one pole is set longer than the other. (Those poles are adjustable length BTW, in case that hadn't been made clear) You shouldnt need to "jam" them up into the peak, to get the pitch tight ... again that comes down to the original placement of the end stakes ... Just adjust the length of the poles to take the wrinkles out of the center of the inner tent side-wall.
For #4 I assume you just mean that little plastic end-cap thing, in which case the cap should not matter as long as you keep the missing end up in the plastic/PVC ridge piece ... you don't want to poke a hole in your floor with an exposed end of pole.
For #5 I'm a little unclear what you mean. What I can say is if you have the cuben floor, it's going to leak eventually. I have the heavy weight CT5K.18 cuben floor, and even it is just too prone to getting holes poked into it. SilNylon has its drawbacks in particular applications, but the advantage of a SilNylon floor is that it will close up on itself a bit when it is poked. My opinions on Cuben-Fiber and its proper applications drastically evolved during my thru-hike. Hindsight is 20/20, but in light of this fact you should use the tyvek to protect and extend the life of the floor IMHO and be ready to periodically patch pin-holes.
For #6 ... Back to #1. Practice.
Hendrik did a pretty good job demonstrating a proper pitch for the solo ... a lot of the basic principals still apply to the So-Long: http://www.youtube.com/watch?v=4ZsbeJsibRo
Here is another one that focuses on the awning in storm mode: http://www.youtube.com/watch?v=b_d3g93itIw
Hope that helps some?
(Here is a pic of a pitch on a really blustery ridge. I have had great success in all kinds of weather including a wind-storm outside Mojave that stripped the roof off the local Motel-6 and 10 inches of wet snow outside Teton NP. You'll get it eventually.)