This is a two part question that I'd really appreciate any help with, I couldn't find previous posts about this so I apologize if this is a repeat question. It all stems from attempting to create this figure that I drew:

where the two blue lines are imported from a data file created with C++, and the grey pencil marks are what I'd like to draw with Tikz. My first question deals with alignment, I'm having issues placing the lines I'd like to draw next to my imported lines. Whenever I try to draw them, the blue imported lines shift. If anyone has suggestions as to how I could draw on an imported curve that'd be great.
My second question is how do I create the arrows behind the blue lines? I know how to create them one-by-one, but I'm sure there is a better way where they stop at the next line they see.
Here's my code, it is able to compile, but definitely doesn't come close to creating my hand drawn image:
\documentclass{report}
\usepackage[top=1in,left=1in,bottom=1in,right=1in]{geometry}
\usepackage{pgfplots}
\usepackage{subfigure}
\pgfplotsset{compat=1.7}
\usetikzlibrary{backgrounds}
\usetikzlibrary{patterns}
\pgfdeclarepatternformonly{north east lines med}{\pgfqpoint{-1pt}{-1pt}}{\pgfqpoint{7pt} {7pt}}{\pgfqpoint{6pt}{6pt}}%
{
\pgfsetlinewidth{0.4pt}
\pgfpathmoveto{\pgfqpoint{0pt}{0pt}}
\pgfpathlineto{\pgfqpoint{6.1pt}{6.1pt}}
\pgfusepath{stroke}
}
\begin{document}
\begin{figure}[!htb]
\centering
\subfigure{
\begin{tikzpicture}
\begin{axis}[
xtick=\empty,
ytick=\empty,
axis lines=none,
no markers,
]
\addplot + table[x index=50, y index=5000]{velocityprofile1.dat};
\end{axis}
\end{tikzpicture}
}
\subfigure{
\begin{tikzpicture}
\begin{axis}[
xtick=\empty,
ytick=\empty,
axis lines=none,
no markers,
]
\addplot + table[x index=3644, y index=5000]{velocityprofile1.dat};
\end{axis}
\end{tikzpicture}
}
\begin{tikzpicture}
\begin{scope}[on background layer]
\draw---(5,0);
\end{scope}[on background layer]
\end{tikzpicture}
\caption{FTCS I}
\label{fig:please work}
\end{figure}
\end{document}
The velocityprofile.dat file is somewhat large and the question isn't really about importing that data specifically so I haven't attached it, let me know if you need it. Thanks for your help in advance!
EDIT: This is my code. The first column is x index=50 in the code, the second column is x index=3644, and the third is y index=5000.

pgfplots? Isn't that what I did, or is there another way? @A.Ellett I tried uploading the data file to pastbin.com but my file size is too big, any other suggestions as to where to post it? – Patamoose Apr 10 '14 at 23:33x index=1for the left image,x index=2for the right image, and for both,y index=3. – Patamoose Apr 11 '14 at 01:04