That CPU will give you some room for a new GPU for the time being. The FX 4170 is a good recommended budget CPU, and the 4100 should be similar.http://www.tomshardware.com/reviews/gaming-cpu-review-overclock,3106-3.html
Also, an upgrade to an FX6300 is not going to be substantial enough to merit the cost of the upgrade, imo.
Don't worry about the board not being PCIe 3.0. PCIe 2.0 limits have not been hit yet unless you're planning on 3-way SLI...which I don't think you are.http://www.hardocp.com/article/2012/07/18/pci_express_20_vs_30_gpu_gaming_performance_review/1
So I'd say go for the video card upgrade now. You're going to get the biggest improvement by going that route. At some point, consider upgrading the CPU. If it were me, I'd wait until you can get a good price on an 8 series part and need to upgrade the GPU a second time.