I don't understand why there is a lane there, that says PCI-E x16. And just has silver dots where the slot should actually be. I'm not trying to upgrade this board as it is a project of mine. It's not my daily computer.
That depends. The motherboard may not support PCI-E, sometimes they'll use the same PCBs for different motherboards. Just because it has a spot for PCI-E doesn't mean that it would support it. If you see any PCI-E options in the motherboard then it might be possible to install a PCI-E slot, but we're talking about a lot of soldering work for something that might not even work.
If its a OEM computer and a lower end one. They have motherboard manufactures make boards as cheap as possible. So the chipset probably supports PCIe but the OEM only wanted it for onboard video. So the board manufacture can take a existing board remove slots and accessories thats not needed cheaper then thay can make a board from scratch. But even if it has the contacts for the slot, it might not have the wiring in the PCB.
This computer has sentimental value to me lol. In 2005 I played on it's 64 mb integrated video card.. and played halo/cs. I'd probably try and pick up an 8400gs for like $20 on ebay for it, and it would make all the difference in the world.