Hi there,
The idea of using a pcie firewire card is fine and, in principle, won't introduce any issues.
Whether or not a given card will be compatible, or play nice, with a given interface is another matter though. Firewire is notoriously fussy on Microsoft platforms.
Whether USB2 is faster isn't really relevant because both exceed the interface requirements by far.
Since you asked, though, USB2 theoretic throughput is slightly faster than that of FW400, but in practice FW generally outperforms USB2 by quite a bit, as far as I know.
I think unless you have (or are buying) a combination that's known to work well together, I'd just go USB 2.
Hope that's helpful.