The differences will be the versions of (WiFi) 802.11 the card can support. As an example the older board won't support 802.11n services like WPA & WPA2 and will be slower.
I would get the newest board the system can support
- 2009/Nehalem MacPro - AirPort Extreme (802.11g)
- 2010/Westmere MacPro - AirPort Extreme (802.11a/b/g/n) Apple P/N 661-4907
Here is one source for the part: OWC - AirPort Extreme 802.11n Wireless Mini-PCIe Card - 661-4907. As you can see this board will work in the older system. I'm not sure if your older board will work in the newer model.
As to removing it from your older system, it's a bit of work as you'll likely need to take the CPU board out as its just below on the backplane. Here's a vid that shows it: Install Airport Card on a Mac Pro.
Unlike the older model were the AirPort card was under the CPU's, the newer model has it located under the PCI slots on the backplane (bottom), which is a lot easier to get to. Heres a vid that shows were it is 2010 Mac Pro Airport Card