I think you are sweating little details. It seems you like the Fuji brand. The differences between models, like most brands come down to the mix of components on the frame, wheels and the frame itself. The mix can consist of a better frame with modest components on it or, conversely a modest frame with better-quality components on it. The result is you agonize over Ultegra-equipped vs Tiagra-equipped, or better frame vs basic frame. This all assumes the geometry between frames is exactly the same.
I suggest, in the price-range you are looking in to pick the mix that makes the most sense to you. It's a personal thing. For me, for example, I prefer Ultegra bits because I am satisfied with the quality of function, thinking Dura-Ace does not meet the bang for the buck criteria I set. I'd rather spend my money on the better frame and better wheelset.
What complicates choices is that many large bike manufacturers mix components on their bikes, choosing Tiagra hubs and such where the quality does not make as much difference vs the brake levers which are prominent and make a bigger daily difference to the look and feel of the bike. Now you can't pick as easily from one model to another in a manufacturer's range since the mix of better and average-grade bits varies on each model.
My best advice IMOHO is that you pick the bike that pleases you the most. One model should fit your compromise criteria best. Another model will require more compromises than another or will compromise in an area where you are not satisfied.
On another topice I sympathize with the theft of your bike. Mine was stolen as well, but mine was in a different price range than yours. My decuctible was also $500 but it was a smaller percentage of my total loss. In my decision-making process there are other things, like the pedals (clipless), seat wedge, tools and a stronger lock.
