Me personally, I think the Fuji at Performance is an absolute steal at that price listed in the link. There are some component trade offs but I think you're getting more bike with the Fuji.
When you say more comfortable with brakes and shifters ... do you mean the actual component itself, or the way it was positioned? Positioning can be changed for your fit
I think you should look at the Lexa S too, as mentioned above. Your LBS may not consider it an endurance/road bike, but it's definitely in the realm and has eyelets and mounts for rear racks etc ... That said, the Fuji still is a better deal unless you can negotiate with your LBS on price for the Spesh or Trek.