Use of underscore outside math mode will confuse TeX. The right fix is to escape the underscore. Unfortunately this is not done automatically, so you have to do it manually. Underscore works right in verbatim blocks and function_names(). Similar problem exists for caret.
I am not a LaTeX- or TeXpert. I wrote this software to avoid learning LaTeX :-) thus there are probably better ways of doing things if you are in the know.
If rendered document starts by "<1sp" after you added
\usepackage{lineno}
\linenumbers
clause, then this is due to ordering dependency between packages. It appears that lineno package needs to appear before longtable, and possibly before fancyhdr. Solution: Use 'lineno' as moreopt parameter of class. Otherwise, you will have to hand construct a texpreamble.