Please just attach the text of the pertinent part of the m-files instead of making us download (yet another) zip file...
findpeaks draws both the line and places the markers on the plot itself; you don't need to draw the line additionally with plot().
findpeaks, however, does NOT return the handle to the lines drawn; if use output variables it then doesn't draw the graph at all and returns the requested information about the located peaks.
So, use findpeaks as I showed before, then before moving on to the next axis, retrieve the line handles and set the properties of those as desired.
IF you do things sequentially, you can get the legend to appear as you want by ordering the line handles in alternating order and having the labels to match.
Of course, you can also use the 'DisplayName' property of the line instead of writing it explicitly in the legend.
ADDENDUM
To reorder the order of variables, just build an indexing array of column number or name in the desired order and use it in the loop to retrieve the next by reference. There's no need to create a zillion temporary variables and write every line of code over and over -- that's the power of having a programming language at your beck and call to be able to generalize instead of copy and paste like a spreadsheet.
Also, if you want a different name for the variables, fix up the 'VariableNames' property to contain them as you want them named -- there's no magic there that they have to keep the name in the file--just they have to be unique.
