A few more comments:
1. Specifying --build should not be necessary, as it should default to config.guess, right? If so, we should document that you cross-compile by passing --host. OTOH, I see it is a bug that you cannot just specify --host...
2. what are the implications of AC_CHECK_TOOLS wrt. the current AC_CHECK_PROGS invocations? There is a lot of logic to determine the C++ compiler...
3. should we include config.sub? Can we share it easily with the libffi one? Where do I get the most recent version of it?
4. Where does the mapping of system names from -dumpmachine come from? What would need to be done to eliminate this altogether? What about ac_sys_release?
5. Isn't there some autoconf way for detecting a C compiler for the build system? It shouldn't default to 'cc'.
6. I don't think the "skipping import check" warning is needed. Just silently don't perform this check.
7. What is the meaning of CROSS_TARGET? In some place, it is used like sys.platform (so it should take one of the possible values for sys.platform), in configure.in, it is set to ac_sys_system.  I think you should just use MACHDEP here.
8. Why is /usr/local/lib excluded when cross-compiling? Please add a comment (likewise for lib64)

Otherwise, it looks fine; I haven't been able to test it yet, though.