This looks good!  Is it worth mentioning that autoreconf updates pyconfig.h.in as well as configure?

There's also an OS X oddity to be aware of, though I'm not sure whether it's worth mentioning in the FAQ.  On OS X 10.6, the system autoconf (/usr/bin/autoconf) *appears* at first sight to be autoconf 2.61 (e.g., using autoconf --version), but has actually been modified slightly by Apple:  it produces a whole bunch of

-rm -f conftest*
+rm -f -r conftest*

differences in the generated configure file.  I don't know how much this really matters---it can make checkins look a bit confusing at times but seems otherwise harmless.  But I've been sticking to GNU autoconf 2.61 and avoiding the Apple version for this reason.

Nitpick: Various occurrences of 2.6.1 in the above should probably be 2.61.