Thanks Richard,
I will patch those resistors and report back here if it works.
In that schematic segment I posted there is also LAN_CLKREQ. I have muxed it as a GPIO, but it is not implemented anywhere in my board-mx6q_sabresd.c.
Is this pin critical for the operation of the PCIe bus?
Here's a segment from the datasheet: http://i.imgur.com/lAfSahM.png