I started with a minimalist setup, using the default Casper theme with a few necessary additions. If you like any of them, here's the resources I used.
Initially, I made all my alterations in the Ghost header through code injection. Eventually, that got too bulky, so I started working on my own theme, which has a corresponding git repository. Eventually, I will link to that here. In the meantime, here's my features, with some of their code.
The stuff that has code here.
- prettify CDN for pretty code syntax highlighting, usable with markdown syntax
- mathjax CDN for pretty LaTeX-style math 
- jQuery CDN for the features below
- handling spoiler text and toggle
- handling external links:
- to open in a new window: when the document is ready, insert this css-tricks code
- to add unicode arrow (↗): insert
$(this).append("↗");inside the conditional statement of the css-tricks code.
The stuff that will have code linked later.
- the table of contents
- to automatically generate: I followed this post
- to get centering right: this guide
- to follow scrolling text: I followed this Q&A and added some CSS and jQuery code of my own
- to add a show/hide button: I added some code inspired by this demo.
- to make sideways/rotated text: (CSS-only) I started with this solution, and then finagled the surrounding divs to match.
- the blue links for expanding hidden text are implemented through jQuery extensions to the markdown syntax, which can be found in assets/js/markdown.extended.js in my theme repository once I link it into here.