I am in the same dilemma as you (I have Fuji S2 + non digital 6X6, 5"X4"), I shoot fashion and advertizing. I decided after checking, to buy the Canon 1Ds mark II 16.6 MP, for it's versatility, high quality and value for money, (8000$). MF 22 Mp digital are ~ 25-30% better in resolution but cost 25000$-30000$
About the firewire connection that has become unstable recently, try the new "plastic rings" solution that came now for the S3 (also 6 Mp resolution). look at it at somebody who has S3 and try to fix such solution to your S2.
regards Menachem www.reiss.co.il