Oh boy, quite a few issues there....
Firstly, i think THE biggest problem will be transsonic drag, which will be HUGE where the SC is planning to fly at. I don't know how Boeing are going to counter that, unless they've got some sorta super-dooper aerofoil they're not telling us about.
You're design looks okay, but there are some problems. Firstly, it doesn't look too big for a 767-size airplane. Secondly, the aerofoil you're drawn looks more supersonic than subsonic, and although that would be magnificent at transsonic and supersonic speeds, landing performance would be AWFUL! Remember, Boeing wants to get this plane in and out of the same runways as current aircraft with similar landing/take-off speeds. If you're going to stick with that aerofoil profile, you need to lengthen the chord, significantly, and if you do that you almost end up with Boeing's design
. Another problem is engines. Where are they? Pylons, like so many others? That would cause BIG problems at transsonic speeds, and semi-buried engines like Boeing's SC design has would be better.
You might want to look at the fin too. I haven't worked it out, but it looks at though the surface area MAY need to be bigger.
Canards and a twin fins are very useful for faster aircraft. Canards give you quite a lot of pitch control at higher speeds and depending on C of G, etc, they can significantly reduce drag compared to a standard stabilizor at the rear. Twin fins helps to maintain stability, especially near transsonic boundaries.
As you mentioned, the biggest problem for Boeing is that a lot of the stuff on the SC is new for them. They've never had twin fins, canards, embedded engines, but i'm sure that if they put their minds to it they can pull it off.
You're design still looks good though, well done!
ps. so you want to work at Boeing?
I'd love to have CATIA and EPIC on my home PC. That would be SO COOL! Ah well, maybe one day...