Arrange multiple TikZ pictures

The scope environment of Tikz is well suited for such tasks, as it allows to shift and rotate everything it contains. My suggestion is to create one tikzpicture and then create a different scope for each axis you have. This leads to a setup like this:

\begin{tikzpicture}

    \begin{scope}
        \input{X}
    \end{scope}

    \begin{scope}[yshift=6cm]
        \input{G_1}
    \end{scope}

    \begin{scope}[yshift=8cm]
        \input{G_2}
    \end{scope}

    \begin{scope}[xshift=1cm,yshift=-0.8cm,rotate=90]
        \input{B_1}
    \end{scope}

    \begin{scope}[xshift=-2cm,yshift=-0.8cm,rotate=90]
        \input{B_2}
    \end{scope}

\end{tikzpicture}

Note: so far, every .tex file includes a \begin{tikzpicture} ... \end{tikzpicture}. For a solution like this here, you need to remove that, so only the axis stuff remains.

The result (shown below) might not be perfect, but by adjusting the shifts, you should be able to get a nice result.

You can simply use a tabular:

\documentclass{article}
\usepackage{pgfplots}
\usepackage{graphicx}

\begin{document}‎‎

\noindent
\begin{tabular}{@{}cccc@{}}
& &  \input{G_1} \\
& &  \input{G_2} \\
\rotatebox{90}{\input{B_1}} & \rotatebox{90}{\input{B_2}} & \input{X} \\
\end{tabular}

\end{document}

The result: