Dear Mark. I continue testing; today I could install MathJax;
and it seems to work well with MediaWiki 1.21.0rc1
The installing was not so difficult, it is mainly straigitforward.
(However, the debris from the previous attempts should be removed.)
I think, you can easy include the MathJax into your package.
As for the ShortURL - not yet.
Few times I tried, but the brouser does not see the ShortURL.
Perhaps, it is not so easy to write the universal algorithm for the installing.
I am about to give up trying to install it in a civilized way.
I have learned some of PHP and HTML, and I can create a set of
directories with corresponding unconditional redirections,
one per each MediaWiki article.
This is brutal and barbarian solution,
but it seems to work independently on the platform;
so, you may consider to write something similar for your tarball.
Definitely, you can do this much better than I do.
(This is my first serious and meaningful PHP script!)
I continue the testing.
While, I see no option to download the *.pdf pictures
nor to include the images from WikiMedia Commun.
I'll search and I hope to find these options in future.