datacursormode and brush help

I'm doing an experiment where I repeat the same test and save the results in separate CSV files. I need to time align the results so they overlay correctly. I plot 2 lines on a graph and ask the user to select the two start points. Right now it works if they select a point from the first file first, and the second file next. I would like to make it more dynamic and have it use a selected point on a line and a range of data from the second line. Compare the first Y1 to the range of Y2's and give the X value that corresponds to the closest Y2 value. I also need to know which line the point came from so I can time shift it correctly. Below is how I'm doing it now (don't be too harsh on the code, I'm a newb)

% This section of code is used for the initial plotting algorithms.

Plots.number=inputdlg('How many parameters would you like to plot?');
Plots.number=str2num(Plots.number{1});

for i = 1:Plots.number(1)
    a='Please enter parameter ';
    prompt=cat(2,a,num2str(i));
    Plots.parameter{i}=inputdlg(prompt);
    subplot(Plots.number(1),1,i)
    plot(Data1.TIME,Data1.(Plots.parameter{i}{1}),Data2.TIME,Data2.(Plots.parameter{i}{1}))
    xlabel('Time (seconds)');
    ylabel(Plots.parameter{i}{1});
    grid on
    l=legend(FileName1,FileName2);
    set(l,'Interpreter','none');
end
%%Time Aligning Events
fprintf('Please click on the start of the events, blue first then green\n');
[x,y]=ginput(2);

%Now, repeat the plotting with a shift in X equal to the difference between
%the two mouse clicks.
TimeShift=(x(2)-x(1));
for i = 1:Plots.number(1)
    subplot(Plots.number(1),1,i)
    plot(Data1.TIME,Data1.(Plots.parameter{i}{1}),Data2.TIME-TimeShift,Data2.(Plots.parameter{i}{1}))  
    xlabel('Time (seconds)');
    ylabel(Plots.parameter{i}{1});
    axislims=axis;
    axis([0 max(Data1.TIME(end),Data2.TIME(end)-TimeShift) axislims(3) axislims(4)]);
    grid on
    l=legend(FileName1,FileName2);
    set(l,'Interpreter','none');

end