Ok, what a mission, but I got there in the end.
In case anyone else ends up following in my footsteps (or I reinstall my machine and can't remember) this is what I ended up doing in addition to the software in my first post:
1. Install the Microsoft Direct X SDK
2. Install the Microsoft Windows 7 SDK (for AMD 64, yeah even if your processor is an Intel 64-bit so long as it isn't Itanium)
3. Add the bin folder from your Qt install to your path variable
4. Start a VS.Net 2010 command prompt and go to the Qt directory
5. Run this command line:
configure -platform win32-msvc2010 -opensource -qt-zlib -qt-gif -qt-libpng -qt-libmng -qt-libtiff -qt-libjpeg -nomake tools -nomake examples -nomake demos -nomake docs -nomake translations -ltcg
6. Run nmake
After a fair time to compile (and lots of warnings scrolling by) it should have finished compiling Qt. At this point I was able to go back to my x86 project for VS.net, rebuild it and finally my own build of Sigil.exe runs. Yay!
I get one warning in the error list in VS.Net (LNK4068: /MACHINE not specified; defaulting to x86) but since it still works I don't care.
Thanks Valloric for identifying the problem and of course for Sigil to dabble with. I was very close to building a VM with VS.Net 2008 in it to save all the hassles but got there in the end.