You got an up-down-grade! Faster CPU, smaller HD and BT/airport absent.
I'd say, for the CPU upgrade, that's a good thing. For the HD, at least, it is easy to add another one and get more capacity than what you had before. But for BT, the module will be difficult to add by yourself... For Airport, Apple have their module on sale on the refurb for cheap. Must be the 802.11G, not sure it is compatible with the Mac Pro.
Maybe just calling Apple and they will send you replacement parts for free!