Firstly, things like automake, autoconf and aclocal are all compiled on FreeBSD with the version number tacked onto the end. E.g. aclocal -> /usr/local/bin/aclocal19 etc.
My solution to this problem was to create a folder (e.g. /etc/symlinks/)
Inside that directory I did:
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ln -s /usr/local/bin/aclocal19 aclocal
ln -s /usr/local/bin/autoconf259 autoconf
ln -s /usr/local/bin/autoheader259 autoheader
ln -s /usr/local/bin/autom4te259 autom4te
ln -s /usr/local/bin/automake19 automake
ln -s /usr/local/bin/autoreconf259 autoreconf
ln -s /usr/local/bin/autoscan259 autoscan
ln -s /usr/local/bin/autoupdate259 autoupdate
ln -s /usr/local/bin/ifnames259 ifnames
Next I added this directory (/etc/symlinks) to my $PATH (in my case I did it in /etc/profile)
After a reboot (just to be safe, I know you can just reload the profile etc or path but meh ) you should be able to type something like aclocal --version and get a response.
The next thing I had to fix were the libtool errors.
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echo '/usr/local/share/aclocal' >> /usr/local/share/aclocal19/dirlist
Hope that helps someone else who is struggling.