The issue with that motherboard and pci-e 2 cards is that the motherboard bios checks the video card bios to see what is plugged in. (if it's agp or pci-e)
basically in the video card bios there's a line that says that it's pci-e 2.0 but the motherboard is looking for pci-e 1.0 or pci-e 1.1
The early solution was to flash and video card bios with a fixed bios that includes pci-e 1.0 and 1.1 in the bios. (although the ati 3xxx series included it so there was no need to flash them, the nvidia 8800gt didn't so needed flashing)
However I seem to remember that the motherboard bios was updated to include pci-e 2.0 so any pci-e 2.0 card should work.
However the fact that it's only pci-e x4 will hold many new cards back, how much depends on the card.
The other issue you may have is that old pentium d holding you back.
If you want to stick with your current motherboard then I'd sugest looking for a 2nd hand c2d 65nm cpu (e6xxx)
If you replace your motherboard then you should also consider getting a e5200.
The ghz rateing in both cases may be lower but it will out perform that old pentium D and will be cooler and use less power.
note: remember a change of motherboard generally needs a re-installation of windows as well.