I finally got around to trying this again and just got it working

I was trying to use it with a clean Cygwin install + Zero's cross-compiler but couldn't get anywhere with it after a few tries.
I then tried it with AmiDevcpp's cross-compiler setup and that works fine so far (maybe you need mingw32).
Very nice so far, I think this is best solution for building AmigaOS C/C++ on win32.