rather than solutions I'm afraid!
The Radeon 9700 pro, as I understand, requires two seperate power connections and so will need a decent power supply and also the (easy?) availability of the second power connection, if you were to fit it.
It is also the case that the 9700 pro can run at 8 x AGP, so to get the absolute most from it you should check that the motherboard will support 8 x AGP. There is also a voltage difference between the types of AGP slot, but I believe the card can cope with that, but it would be worth checking.
Whenever you order a PC from anyone you should always confirm the precise details in writing, and not just order Model xxxy. The model details can change put if you specify what you are ordering and they do not supply it, they are clearly in the wrong!
I can't comment on shortages, but lots of places are advertising it!