Your CPU, motherboard and video cards are well balanced for gaming. You can rest easy with the rig.
I have a chart I am working on for a R9 Fury which runs fine even with PCI Express 1.1 x4 so do not worry with PCI Express 2.0 x8 slots.
Guru3D did a good article comparing PCIe 1.1 x16 to PCIe 2.0 x16 to PCIe 3.0 x16 with the nVidia GTX 980 last year at 2560x1440, which is about 20% faster than the R9 290, in both single and SLI setups. PCIe 1.1 x16 = PCIe 2.0 x8 = PCIe 3.0 x4 in terms of bandwidth. There is technically a "bottleneck" of sorts in SLI, but it varies from between near 0% in Firestrike to 20% in Thief, with an average result of about a 10% speed reduction, but even then the frame rate is well above 60.
TechPowerup last year did a PCIe 1.1 vs 2.0 vs 3.0 comparison with the FuryX, but sadly neglected to do a Crossfire test, but even if the additional burden of handling Crossfire via PCIe reduced the effective bandwidth to PCIe 2.0 x4 levels, performance reduction would still be less than 10% loss vs x16
So don't worry about it.