Dina,
Here are a few things to check.
- A5/B5 should be connected to the PLX 8311's TX lines through capacitors (standard PCIe levels). TX --> cap --> A5/B5
- C5/D5 should be connected to the PLX 8311's RX lines (standard PCIe levels). RX <-- C5/D5
- Refclk is not a standard PCIe level. It's LVPECL instead. So it should should be AC-coupled and rebiased/terminated. As I recall, this suggested bias is a 56 ohm resistor to GND and a 475 ohm resistor to 3.3V (50 ohm Thevenin equivalent, center point of voltage around half the normal swing of PCIe's HCSL clock lines). The PLX bridge may have different requirements. RefClk <-- [bias resistors] <-- cap <-- E4/F4
- PRSNT# (A2) should be pulled down or connected directly to GND, though it's not used in a 1073.
Robert