Difference in FPS

Solution
You want to put your card in the first slot, the pcie 3.0 slot operating at x16
If you put it in the other x16 slot, it will operate at X4
Your GTX760 will not fit in a pcie slot.
If your graphics card is using a pci slot, it will not be compatible with a pcie slot.

Modern pcie graphics cards are stronger and cheaper, so replacing your graphics card would likely be a big upgrade.
What is your motherboard, graphics card, and psu now?