Whilst having 2 automake's on your system isn't generally a good thing, and you have probably fixed the immediate problem, for future reference you can probably do (under bash, I don't know csh):
AUTOMAKE=/path/to/automake AUTOCONF=/path/to/autoconf AUTORECONF=/path/to/autoreconf (etc.) ./configure <options>
I know the FreeBSD guys use this.
Alex
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