Yes, I'd definitely advise going with an Athlon 64
The 3200+ should be around 200$ and the 3000+ is ~150, with an nForce4 Ultra mobo being ~110 or a plain nForce4 board being ~80.
It'll almost certainly be faster, not to mention you have an easy upgrade path to dual core if you want to later, since it uses the same socket. You might as well go with PCI-E in that case, as there's not too much of a reason not to. (And it looks like there are some nearly identical PCI-E quadros, at nearly the same price, but I really have no clue about workstation cards)
Only other observation is I have no clue how much I'd trust the power supply that comes with that case, as it seems to be genericly branded by a case manufacturer I've never even heard of.