Let's start with the basics and you tell us what drivers you have installed and from whence you got them.
I just finished my new build(msi z87g45, 8gb gskill ripjaws ddr3 1600, evga gtx 760 sc, intel i5 4670k, corsair rm 750) with a new windows 7 installation and it has been much slower than I had hoped. It runs games well except for some minor stuttering even when the fps is high. I used all the benchmarks and tests I could find and they were all in the range they should be. But when I open folders and programs it seems they take like twice as long to load, and the animations also lag a little. When I launch chrome the home page with bookmarks take over 2 seconds to appear, and it's the same when opening new tabs. Could it be my hard drive(its like 4 years old)? Drivers? Should I run more tests(I've run memtest86, hdtune, performance test 7, heaven 4.0, intel processor diagnostic tool)?