LaTeX.org

In general you should avoid absolute paths in sources (they make them non-portable): something like export TEXINPUTS=/server/path//: should allow just \input{file}.

I'm not sure I really see the LaTeX link here: can you give a bit more detail?

The idea of separate layers is very important in the work being done by the LaTeX3 Project. \NewDocumentCommand and relatives are for defining document level commands, so 'things you use in a typical LaTeX file'. On the other hand, \cs_new_protected:Npn and so on are 'code level' functions for ...

As noted, the achemso class is for submissions to the American Chemical Society, not for journals published by the American Institute of Physics. For the latter, you should use REVTeX.

As detailed for example in http://serverfault.com/questions/16355/how-to-set-global-path-on-os-x, on the Mac the location /etc/paths.d can contain a series of files each of which add exactly one entry to the global path. The files can have 'user friendly' names, so the one that adds the TeX system ...

Babel stores information between runs in the .aux file. Delete that and try running your file again (twice).

Achemso doesn't use expl3 at all, so you mus have something else going on. It looks like a package version mismatch, but without some code it's impossible to say.

I'm perhaps being dim here: what is the expected difference between those two x's?

Test using \detokenize is expandable and therefore more general.

The \twoside option is about layout: if all you are doing is printing on both sides of the paper and don't want/need the visual distinction you could just not do this.