The current Fuji has a 11-34 cassette,. If the 2009 is the same the derailleur would have enough chain wrap but you would probably have to take a link out of the chain.
I don't like "brifters" and wouldn't hesitate to change them long before they're worn out. My favorite is downtube shifters but the Fuji doesn't have the right kind of braze on.
A seatpost rack places the panniers higher, farther away from the feet.
I'm 6' with a 32" inseam and I like a 58cm top tube or longer. Maybe my arms are longer than yours.
I have no trouble straddling a bike with a 58cm seat tube and a level top tube.
700c wheels ride better. If you're worried about wheel strength get some 29er rims.