In addition to @oliversm answer, the memoir class (a superset of book and report) provides many means to enhance the appearance of your thesis. The documentation (> texdoc memoir) describes, and provides the code for, an example book design and a thesis design.
Some of the obvious ones
There are several obvious ones, such as amsmath, and a few of the ones you have mentioned. Of course it would be remiss not to mention the physics package, although it is a bit of a matter of taste (cf. Alternatives to the physics package), although I generally like it.
Some of the less obvious
Some of the tools I have found great ...
I am now not so sure anymore, as the jupyter-markdown loses points in terms of flexibility and things you can actually do.
You have not given us clues whether you use R in your notes, and moreover I do not know Jupiter well enough to compare, but considering the above cite in the context of maths thesis, then indeed, your tool is Rmarkdown in Rstudio, ...
Perhaps try deleting all of the auxiliary files (e.g. ending in log, aux, dvi, lof, lot, bit, idx, glo, bbl, ilg, toc, ind, out, blg, which is pretty much everything that doesn't end in tex, albeit with a few exceptions), and then recompiling. Most IDE's (such as TexStudio have a button for this in their Tools tab).
Instead of commenting the lines, try
that is, with an empty space between the brackets.
It's likely that Thom Jackson and My Nominating Professor are the default values of the commands.
Here's one way to do it. The basic idea is to have a single command:
This will automatically assign membership of the committee, and keep track of how many there are. Then each committee name/affiliation is given a unique name using the counter that keeps track of the members. This is done using the \csgdef wrapper ...