I increased the base clock in my BIOS from 100 to 100.1. I've read that increasing the base clock can damage anything in the PCI-E slots. Could this small adjustment damage the GPU?
It can, but it will destabilize your system before it does that. I don't suggest increasing it as it adjusts to your multiplier settings. If I recall, BCLK is used more for memory OC'ing, which I am not familiar with.
Are you talking about the PCIe Express Frequency on LGA 775?
What kind of setup are you referring too?
LGA 1155.
Then I don't suggest going over 105-107 Mhz unless you are using LN2 which I doubt