Fuji's ROCK, Dude! Even though I have moved on to a nicer bike, I couldn't bear to part with my trusty Fuji.
First thing is to get some padded shorts, they will really help to keep you comfortable. If you have comfort troubles, you might also want to try different saddles. Minor fitting problems can be overcome by adjusting the saddle posiiton and the stem.
Don't know what kind of riding you are planning on doing, but I guess one thing I can say is to learn to use your gears. Keep your cadence up. A resource I always enjoyed was Harris Cycles
Welcome to the world of the roadie, enjoy!