Addendum:

> SATA controllers on P5 must be enabled, thus x4 x4 x1 x1 PCIe config is best

Seems like that's exactly the PCIe configuration A-Eon is using on the Cyrus board:

http://amigaworld.net/modules/newbb/viewtopic.php?topic_id=38284&forum=2&start=100#719786

(One x4 will have x16 slot, just like done on Sam460ex, only that with QorIQ P5 it's PCIe 2.0 instead of PCIe 1.x with PPC460EX. This also means PCIe bandwidth for graphics on Cyrus is half that of Nemo's PCIe 1.x x16.)