As an aside, to compile with a different prefix using cygport requires a
bit of work right now, because AFAIK cygport doesn't support anything
but --prefix=/usr.
See
http://cygwin.osuosl.org/release/autoconf/gcc-tools-epoch2-autoconf/gcc-tools-epoch2-autoconf-2.64-1-src.tar.bz2
for how I did it. Basically I had to copy cygport's cygconf() function
and modify it, ditto cygports cyginstall() function. Then, from my
src_compile() and src_install() I called my copies.
That's what was needed to put autoconf into /opt/gcc-tools/epoch2/ but
other, more complex packages -- and they don't get much more complex
that gcc! -- might need even more custom overrides.