816x as EP for PC host

I have an 8168 booting from NOR flash. I'm trying to setup PCIe communication by essentially replicating what the ROM code does in Linux. I boot up the 8168 to Linux, insert a module that enables the PCIe 250MHz clock and change the PLL configuration from PCIE_CFG, then I run the following commands to setup the PCIe configuration:

# BAR1 -> region 0

./dumpmem 0x51000300 w 0x01

./dumpmem 0x51000304 w 0x80800000

./dumpmem 0x51000308 w 0x00000000

./dumpmem 0x5100030C w 0x40400000

# BAR2 -> region 1

./dumpmem 0x51000310 w 0x02

./dumpmem 0x51000314 w 0x81000000

./dumpmem 0x51000318 w 0x00000000

./dumpmem 0x5100031C w 0x08000000

# BAR3 -> region 2

./dumpmem 0x51000320 w 0x03

./dumpmem 0x51000324 w 0x81800000

./dumpmem 0x51000328 w 0x00000000

./dumpmem 0x5100032C w 0x80000000

# BAR4 -> region 3

./dumpmem 0x51000330 w 0x04

./dumpmem 0x51000334 w 0x82000000

./dumpmem 0x51000338 w 0x00000000

./dumpmem 0x5100033C w 0xC0000000

# Lane x1 only

# PL_LINK_CTRL

./dumpmem 0x51001710 w 0x10120

./dumpmem 0x5100180C w 0x20F

# Set Vendor ID

./dumpmem 0x51001000 w 0xB800104C

# CLASSCODE_REVID

./dumpmem 0x51001008 w 0x401

#MSI_CAP

./dumpmem 0x51001050 w 0x817005

#PCIe CAP

./dumpmem 0x51001070 w 0x020010

I then enable link training using:

./dumpmem 0x51000004 w 0x07

At this point, I'm still able to dump the DEBUG0 and DEBUG1 registers using:

./dumpmem 0x51001728

I turn on the PC and the device fails to enumerate. I'm also unable to read 0x51001728:

# ./dumpmem 0x51001728

/dev/mem opened.Unhandled fault: external abort on non-linefetch (0x1018) at 0x40127728

Memory mapped at address 0x40127000.

Bus error 

Are there any configuration registers that I might be missing? Also, I'm not able to see the status of the link training state machine. Any advice for debugging?