Step 2 seems to work for the non-optional libraries except for openfst for some reason... To get openfst to work I installed it via homebrew (version 1.3.3), I think kaldi by default would install version 1.2.10 ... is this a problem?
Yes, it is a problem. To understand what went wrong you need to study build log. To get help on build issues you need to provide build log with the problem.
Anyway, assuming that kaldi can work with this openfst as well, I tried to run configure in the src directory like $ cd ../src; ./configure; ... but the configuration command always returns 'You must run "configure" from the src/ directory.'
You are probably missing some dependencies, for example you might miss basename binary and that would break the script. You can add
set -x
to configure script to find out what was wrong exactly to collect commands trace. Running complex software on Mac without understanding how shell works is like shooting yourself in the leg. Try to run on Linux or prepare to understand what the script actually does.