kougar
My immediate guess would be that something got into the PCIe slot itself and is fouling some pins. Ya should snag a flashlight and have a very close look inside the slot itself for either stray TIM, fibers, dust, or anything really. The card itself doesn't show up or work at all period, no BIOS and no picture in the main slot?
 
If you absolutely can't find anything you might try cleaning the pins. Compressed air first, then if that doesn't work then MAYBE a strip of cardboard with a paper towel wrapped around it? Clean pencil erasures are recommended for the PCIe connectors on the cards themselves, but I'm not sure what the best material is for cleaning inside the slots. You need to be careful not to cause a static discharge obviously, while still rubbing any possible oxidation off the pins.

Blizzie
Do you have another video card or any PCI-E card to test if the first slot is busted somehow? Put your video card in the second slot and a different card on the first. See if that PCI-E card can be detected in Windows.
 
Did you gently blow some air into the first slot to clean off any dust particles? Also, clean the gold fingers on your video card with isopropyl alcohol.

Baltothewolf

KenMcC
The damage to the CPU may be internal, thus sooooo small you will not be able to see any issue / broken leads.  

Yea I'm thinking I may have done damage. What I don't understand is, wouldn't I be seeing other problems? Doesn't the northbridge control other things as well?
 
Also, I did scratch the PCB twice, here is a pic, sorry it's blurry but I couldn't get my camera to focus.
 

kougar
Modern systems have the ability to disable or ignore non-functioning parts... I mistakingly bent a socket pin on an X58 board, and the system simply disabled one of the three memory channels. The system could see the memory and it would show up under the OS, but it was marked "hardware reserved", in other words effectively disabled. The system ran error free because it self-corrected for the hardware damage. 
 
I didn't honestly think of it but I should have. Wmmills is probably spot on. The PCIe controllers are just another uncore I/O component and not critical to the function of the processor or system. It probably just disabled the affected controller to ensure it would operate error free.
 
Assuming for the moment it is a damaged chip, there's a bit of good news. In all honestly, even 4x at PCIe 3.0 speeds is the same as PCIe 1.0 at 16x. For a 470 model card you won't notice the loss of performance, except maybe in synthetic testing.
 
That said, if you absolutely want higher slot speeds regardless you may be in luck. That proc has the option for either 1 x16 or 2 x8 PCIe slot configurations, so with a 2 - x8 capable motherboard you might be able to run the CPU at PCIe 3.0 x8 on the secondary slot. The bad news is Biostar doesn't have any settings for this in its BIOS, you'd need a different motherboard. If you can get yours hands on another board you can test this fairly quickly.