OK, I think I have something. If AC_CONFIG_AUX_DIR is populated, automake runs in 9-15 minutes of wall-clock time.
If it is not populated (except for ltmain.sh) then it takes 45 minutes to run. The items that end up in AC_CONFIG_AUX_DIR are: compile* config.sub* install-sh* missing* config.guess* depcomp* ltmain.sh ylwrap* Does this help at all? H
