Here is a copy of the lspci file you needed.
00:0f.0 IDE interface: VIA Technologies, Inc. VIA VT6420 SATA RAID Controller (rev 80) (prog-if 8f [Master SecP SecO PriP PriO])
Subsystem: VIA Technologies, Inc. VIA VT6420 SATA RAID Controller
Control: I/O+ Mem+ BusMaster+ SpecCycle- MemWINV- VGASnoop- ParErr- Stepping- SERR- FastB2B- DisINTx-
Status: Cap+ 66MHz- UDF- FastB2B+ ParErr- DEVSEL=medium >TAbort- <TAbort- <MAbort- >SERR- <PERR- INTx-
Latency: 32
Interrupt: pin B routed to IRQ 20
Region 0: I/O ports at ff00 [size=8]
Region 1: I/O ports at fe00 [size=4]
Region 2: I/O ports at fd00 [size=8]
Region 3: I/O ports at fc00 [size=4]
Region 4: I/O ports at fb00 [size=16]
Region 5: I/O ports at f400 [size=256]
Capabilities: [c0] Power Management version 2
Flags: PMEClk- DSI- D1- D2- AuxCurrent=0mA PME(D0-,D1-,D2-,D3hot-,D3cold-)
Status: D0 PME-Enable- DSel=0 DScale=0 PME-
Kernel driver in use: sata_via
Kernel modules: sata_via
00:0f.1 IDE interface: VIA Technologies, Inc. VT82C586A/B/VT82C686/A/B/VT823x/A/C PIPC Bus Master IDE (rev 06) (prog-if 8a [Master SecP PriP])
Subsystem: VIA Technologies, Inc. VT82C586A/B/VT82C686/A/B/VT823x/A/C PIPC Bus Master IDE
Control: I/O+ Mem+ BusMaster+ SpecCycle- MemWINV- VGASnoop- ParErr- Stepping- SERR- FastB2B- DisINTx-
Status: Cap+ 66MHz- UDF- FastB2B+ ParErr- DEVSEL=medium >TAbort- <TAbort- <MAbort- >SERR- <PERR- INTx-
Latency: 32
Interrupt: pin A routed to IRQ 20
Region 0: [virtual] Memory at 000001f0 (32-bit, non-prefetchable) [size=8]
Region 1: [virtual] Memory at 000003f0 (type 3, non-prefetchable) [size=1]
Region 2: [virtual] Memory at 00000170 (32-bit, non-prefetchable) [size=8]
Region 3: [virtual] Memory at 00000370 (type 3, non-prefetchable) [size=1]
Region 4: I/O ports at fa00 [size=16]
Capabilities: [c0] Power Management version 2
Flags: PMEClk- DSI- D1- D2- AuxCurrent=0mA PME(D0-,D1-,D2-,D3hot-,D3cold-)
Status: D0 PME-Enable- DSel=0 DScale=0 PME-
Kernel driver in use: pata_via
Kernel modules: pata_via
-----------------------------------------------------------------------------------------------
And regarding the message about swapping out parts and the old pci controller.
the old pci controller is irrelevant as I'm now using the on board controller build in to the new motherboard.
I keep wondering if the problem is due to the way the hard drive controls the power and sin up and down. as its supposed to be a low power energy efficient hard drive. which regulats its own platter speed and energy usage.
http://www.wdc.com/en/products/Products.asp?DriveID=336
But I dont know how this is controlled and if it can be altered.
Just another note there are no other hard drives or cd drives connected to the motherboard.
Only this one WD (WD10EACS) drive connected the the master SATA port.
Are there any other logs I can look at that have infomation on the hard drive itself.