What fork do you have with that frame? The carbon-triangle bikes came with a fork that looks decidedly less sturdy than the standard S-works fork. I have the same bike and was going to upgrade, but never got around to it. I ride a 62cm frame and it's been fine, but it's definitely a different component than a factory spec'd E5 S-works. The paint/decal work is also a little different on the team bike, but that's not really a "significant" difference to me.
The carbon rear is a nice touch but I can't really tell that much difference over the standard full-Al bike. I think both bikes are awesome all-'round racing machines, especially for the money. That being said, I wouldn't sell one to get the other....pretty similar in my book.