I previously replied to this post but for some reason it was removed.
If you can, I would recommend test riding both bikes over the usual terrain that you ride. There will be plenty of people singing the praises of both bikes, because both are very good, but ultimately it comes down to personal preference.
I love my Cervelo R3 but have not ridden the Fuji. The bottom bracket stiffness of the R3 is immediately evident as it seems as though that every watt put through the cranks is transferred immediately to the drive chain. A very responsive bike, particularly on the hills. It is also surprisingly comfortable for such a stiff bike, but that is because of the rear stays. I wouldn't hesitate to recommend the R3, but also suggest that you test ride both bikes.
The one that fits the best. If they both do, ride each for an extended ride and decide. If they are a wash, often you 'buy' the bike shop that does the best in fitting, service after the sale, knowledge, real knowledge, not marketeer hype.
If you plan on owning the bike for a long time then don't overlook the warranty. I do not know what the warranty is on these bikes but if all else is the same for you then go for the bike with the best backing.