Both scipy and numpy working fine here (Python 2.7.6 x64).
>>> import scipy
>>> scipy.test()
Running unit tests for scipy
NumPy version 1.8.1
NumPy is installed in C:\Python27\lib\site-packages\numpy
SciPy version 0.14.0rc2
SciPy is installed in C:\Python27\lib\site-packages\scipy
Python version 2.7.6 (default, Nov 10 2013, 19:24:24) [MSC
v.1500 64 bit (AMD64)]
nose version 1.3.3
....
Ran 16575 tests in 136.936s
OK (KNOWNFAIL=277, SKIP=1181)
<nose.result.TextTestResult run=16575 errors=0 failures=0>
Have you tried using Christoph Gohlke's pre-compiled binaries[1]? Here's the list of libraries I have installed [2].
Also don't customize any install paths; leave it everything as default (e.g., C:\Python27). I've long gave up trying to keep my root folder under control; now it's a festival of Ruby, MinGW, Vagrant, etc.
This is the only way to install python libraries under Windows without pulling your hair out. Any other way is truly a nightmare. That's why I use Linux whenever possible for most of my coding.
[1] http://www.lfd.uci.edu/~gohlke/pythonlibs/
[2] http://imgur.com/WahewF2