Okay, you seem to have a pair of problems.
First, --prefix=/usr and so forth aren't commands to be executed directly. That's why you're getting the error. Instead, these are configuration directions (parameters) for the configuration program.
So, the line from the article you need to mimic is:
[benlev:~/php-4.3.0] adam% ./configure --prefix=/usr --sysconfdir=/etc
--localstatedir=/var --mandir=/usr/share/man --with-apxs --with-zlib
As you see, we prefix those params with "./configure", cause we're calling the configure program.
Second, there's the issue of not being able to use LDAP and libXML. This is so new, it's hard for me to guess your exact problem. I do know "gd.h" is not a file for either of these extensions, but for the GD extension -- you should only see this if you pass in --with-gd. Try reading the earlier postings on this board and see if that helps solve the GD problem and you can get everything to work.