Thanks! Those scores are decent enough to play KSP. The fact that you had no stuttering on cloud gate but stuttering in KSP sort of implies that the fault is more with KSP than your computer. Do you have any other 3D video games you can launch and test? How do they perform? There are some free-to-play games you could download from Steam just to compare.
Your physics score is good, actually. Mine is about 4600 on a Core i5 Ivy Bridge (4 cores compared to your 16) and it plays KSP extremely smoothly, but I have a newer graphics card (GTX 950) that puts my graphics score in the 15,000's.
It's still not exactly clear what the problem is. If it were me, I'd start experimenting with removing components. What happens if you take out all but 1 RAM DIMM? (8GB is enough to run KSP -- honestly 128 GB is complete overkill) What if you restrict KSP to only 4 threads on one of your CPUs by setting its process affinity? (Here's how you do that: http://www.howtogeek.com/121775/how-to-force-windows-applications-to-use-a-specific-cpu/) Are you able to fit your graphics card in the PCIe x16 slot after you remove some RAM? If so, does that improve the game's performance?