What is this /etc/make.conf file? What does it control?
Would it be possible to upgrade X to 4.2.0 or 4.2.1? I know the documentation says that 4.0.2 works, but I haven't tried anything that old since driver version 0.9-769 or so, I think -- a long time ago, in other words. Gentoo's portage should have a way to upgrade X for you, which might work.
Can you also post /etc/X11/XF86Config-4 (if it exists, if not, the /etc/X11/XF86Config)?