If two armies arriving on the same day, which one is attacking/defending?

In the .log file you will find the warnings

LaTeX Warning: Label `Fig3Legend' multiply defined.

LaTeX Warning: Label `Fig3Legend' multiply defined.

What this means is that the Fig3Legend label is applied to all three groupplots, and therefore the \ref will point to only the last of these, the last groupplot. As that only has six plots, you get six entries in the legend. One workaround is shown below. I first define eight styles for the plots (for convenience, this isn't strictly necessary), and in the last groupplot I add two \addlegendimage, which is used to add additional entries in the legend.

Note that I also altered the style of +Resources and ++Resources slightly, so there less chance of confusion. You had three lines with the same style.

\documentclass[border=2mm]{standalone}
\usepackage{pgfplots}
\usepgfplotslibrary{groupplots}
\usetikzlibrary{pgfplots.groupplots}

\pgfplotsset{compat = 1.12}

\begin{document}
    \begin{tikzpicture}[
            HA/.style={black, mark=o,line join=round, mark repeat=50},
            CAG/.style={black, mark=x,line join=round, mark repeat=50},
            Rnd/.style={black, mark=|,line join=round, mark repeat=50},
            P/.style={black, densely dashed, mark=square,line join=round, mark repeat=50},
            PP/.style={black, thick, mark=square,line join=round, mark repeat=50},
            PPPT/.style={black, mark=triangle,line join=round, mark repeat=50},
            PPSM/.style={black, mark=square,line join=round, mark repeat=50},
            PPBM/.style={black, mark=asterisk,line join=round, mark repeat=50}]

        \begin{groupplot}[
            legend columns=4,
            legend style={nodes={font=\tiny}},
            legend entries={Hold All,Come and Go,Random,+Resources,++Resources,++ResourcesPT,++ResourcesSM,++ResourcesBM},
            legend to name=Fig3Legend,
            group style={
                group name = fig3_plots,
                group size=3 by 1,
                xlabels at=edge bottom,
                ylabels at=edge left
            },
            width=\textwidth,
            legend style={draw=none},
            xlabel = {\footnotesize $\alpha$},
            ylabel = {\footnotesize Avg Portfolio Value},
        ]
        \nextgroupplot[title={\scriptsize +Resources},
            y tick label style={
                font=\tiny,
        /pgf/number format/.cd,
            fixed,
            fixed zerofill,
            precision=0,
        /tikz/.cd
      },
            footnotesize,
            x tick label style={
                font=\tiny,
        /pgf/number format/.cd,
            fixed,
            fixed zerofill,
            precision=0,
        /tikz/.cd
    },
        ymin=0,
        xtick={1000,2000,3000,4000}]
            \addplot+[HA] table[col sep=comma, y=HoldAll, x=Alpha]{ElicitedFixedAlpha.csv};
            \addplot+[CAG] table[col sep=comma, y=ComeAndGo, x=Alpha]{ElicitedFixedAlpha.csv};
            \addplot+[Rnd] table[col sep=comma, y=Random, x=Alpha]{ElicitedFixedAlpha.csv};
            \addplot+[P] table[col sep=comma, y=Plus, x=Alpha]{ElicitedFixedAlpha.csv};
        \nextgroupplot[title={\scriptsize ++Resources (Empirical CDF)},
            y tick label style={
                font=\tiny,
        /pgf/number format/.cd,
            fixed,
            fixed zerofill,
            precision=0,
        /tikz/.cd
      },
            footnotesize,
            x tick label style={
                font=\tiny,
        /pgf/number format/.cd,
            fixed,
            fixed zerofill,
            precision=0,
        /tikz/.cd
    },
        ymin=0]
            \addplot+[HA] table[col sep=comma, y=HoldAll, x=Alpha]{ElicitedFixedAlphaPlusPlus.csv};
            \addplot+[CAG] table[col sep=comma, y=ComeAndGo, x=Alpha]{ElicitedFixedAlphaPlusPlus.csv};
            \addplot+[Rnd] table[col sep=comma, y=Random, x=Alpha]{ElicitedFixedAlphaPlusPlus.csv};
            \addplot+[PP] table[col sep=comma, y=PlusPlus, x=Alpha]{ElicitedFixedAlphaPlusPlus.csv};
        \nextgroupplot[title={\scriptsize ++Resources (Elicited CDFs)},
            y tick label style={
                font=\tiny,
        /pgf/number format/.cd,
            fixed,
            fixed zerofill,
            precision=0,
        /tikz/.cd
      },
            footnotesize,
            x tick label style={
                font=\tiny,
        /pgf/number format/.cd,
            fixed,
            fixed zerofill,
            precision=0,
        /tikz/.cd
    },
        ymin=0]
            \addplot+[HA] table[col sep=comma, y=HoldAll, x=Alpha]{ElicitedFixedAlphaPlusPlus.csv};
            \addplot+[CAG] table[col sep=comma, y=ComeAndGo, x=Alpha]{ElicitedFixedAlphaPlusPlus.csv};
            \addplot+[Rnd] table[col sep=comma, y=Random, x=Alpha]{ElicitedFixedAlphaPlusPlus.csv};
            \addlegendimage{P}
            \addlegendimage{PP}
            \addplot+[PPPT] table[col sep=comma, y=PlusPlusPT, x=Alpha]{ElicitedFixedAlphaPlusPlus.csv};
            \addplot+[PPSM] table[col sep=comma, y=PlusPlusSM, x=Alpha]{ElicitedFixedAlphaPlusPlus.csv};
            \addplot+[PPBM] table[col sep=comma, y=PlusPlusBM, x=Alpha]{ElicitedFixedAlphaPlusPlus.csv};
        \end{groupplot}
        \node (fig3_Legend) at ($(fig3_plots c2r1.center)-(0,2.5cm)$){\ref{Fig3Legend}};
    \end{tikzpicture}

\end{document}

Yes. You can use the pathauto module.

http://dgo.to/pathauto

With help from @AndreJ, the key was to change to the correct EPSG code:

import pyproj
p = pyproj.Proj(init='EPSG:28991')
lon, lat = p(124616.1535508, 486555.4631204, inverse=True)
print(lat, lon)

EDIT: To find the right EPSG code go to http://spatialreference.org/ and type in your location. Then try each one, for me it was the last one.