Segmented pci bus means that the motherboard has two pathways to handle the data going through the pci bus. This isn't really an issue anymore with PCIe technology. Todays motherboards can handle all the data with ease.
You needed segmented pci bus for running mojo and another firewire device or external firewire storage. You should be able to run mojo on the system you described. Be prepared that running central storage over a network requires constant monitoring and support. Its not difficult to do, but catching and fixing problems early will save you from heartaches and frustration.