> there is no easy way to put a 2nd x16 PCIe card into an X5000
> because there is only a single x16 slot

Indeed. ATI/AMD Fire* PCIe x1 cards may be the easy way to go, then.

> PCIe Riser [...] leads to other mechanical problems.

This thread has examples of PCIe x1-to-x16 risers and PCIe x4-to-x16 cables that seem to work well with PCIe x16 graphics cards in the X5000 standard case.

> it would be nice to have the software fixed to make it possible

Absolutely.