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Posting my own answer. If you use what 'Lockstep' posted at http://tex.stackexchange.com/questions/56839/chaptername-is-used-even-for-appendix-chapters-in-toc , the .cls file can be left as is, and the code that 'Lockstep' wrote:

\usepackage{tocloft,calc}
\renewcommand{\cftchappresnum ...

Haha, thanks for your condolences! This is the last edit I have to make in the document, so I think I'll stick with this version, unless it would be much easier to switch. I should admit that I am very new to LaTeX, so I might be making some very beginner mistakes. Let me know if there is any other ...

My University requires that the chapter and appendix names in the table of contents have 'Chapter' and 'Appendix' before each chapter #. I'm lost as to how to accomplish this, I've read the "LaTeX for Complete Novices" chapter referring to this issue, but am having trouble implementing it with the ...

That did the trick, thanks. I had a lot of packages in the .sty file for some reason, as soon as I moved them over to the main.tex file everything worked.

I am attempting to create a document-wide definition for my Master's Thesis:
\DeclareSIUnit\micron{\micro\meter} which uses the SIunitx package. I am not able to place this definition at the head of Ch. 1, and can't find a suitable place for it in the main.tex, or Thesis.cls files. According to the ...