In the 1990s I wrote I program running on MS-DOS which used a product called Personal Computer High Resolution Timing (PCHRT) by a company called Ryle Design, in Mt. Pleasant, Michigan.
Their product provided a library of routines that provided micro-second resolution. It worked beautifully, by interfacing directly with the 8253 or 8254 timing chip found in PCs back in those days.
If you can track down Ryle Design, they may have found a way to provide high resolution timing under Microsoft Windows.
When Windows replaced MS-DOS I had to abandon that product and moved my product into custom hardware using a microcontroller to achieve high-resolution timing. I couldn't find a way to get high-resolution timing under Microsoft Windows.
This article, although many years old, may help:
http://msdn.microsoft.com/en-us/magazine/cc163996.aspx