Just a thought ... Keep different versions of the autotools (autoconf, automake, and libtool) in different autoconf directories (for eg, autoconf-2.52, automake-1.5b, and libtool-1.4d could be installed in /local/autoconf-2.52).
In addition, each package has its own bootstrap script that invokes aclocal, etc. Further, have the bootstrap script check if the right automake, eg, is being picked up. If not it would set the PATH variable to point to the proper /local/autoconf directory. - Ted
