G'day perlynewby,

Some general pointers:

• Have the Tk documentation open and refer to it often when coding.
• Check the Widget Demo (type widget on the command line) for code that does the sort of thing you want; then adapt for your specific needs.
• Follow the "Clone repository" link and look for code in t/ (test) directories. This may have something similar to what you need.
• Avoid monolithic scripts. Break you code into manageable units (subroutines). Pass references to variables. Declaring lexical variables with file scope is (almost) the same as using global variables: you'll encounter much the same problems.
• Post multiple questions here, each targeting a specific issue. You've asked about checkboxes, file browers, emailing, logging and so on: some people may not have time to answer all; some may not wish to work through everything and pick out the bits they can answer; and others may find a huge wall of questions too daunting and just move on.

For your "Formatting challenges" questions, I suspect your main problem here is the exclusive use of the Tk::pack geometry manager. Laying out the frames of your GUI with pack() is often a good way to go. When lining up widgets within those frames, Tk::grid is possibly a better choice. See the "Tk Geometry Management" section for other options.

For your other questions, it wasn't clear whether you were asking how to do something or how to position a widget (e.g. "on right side below checkboxes"). I've provided tentative answers based on "how to do" and not "how to position".

• "additional pop up check box" — it's unclear what you're looking for here: pop-up menu?; dialog box?; Tk::Toplevel?; something else? I'd guess you'd want the -command option of Tk::Checkbutton.
• "add a file browser button" — see "Common Dialogs" in the Widget Demo.
• "add a button/code ... to email recipients" — Tk::Button with the -command option.
• 'add frame ... to allow user to add comments with a title=> "Special Notes"?' — Tk::LabFrame with -label => 'Special Notes'; Tk::Text for the comments.

Some final notes:

• Please provide error messages or a better description of problems. Things like "my file browser sort of works but requires a lot of work" and "GRRR! -command isn't working for me here" do not help.
• A simple bit of ASCII-art is often a much better way to convey a layout than a prosaic description.
• Please check the code you are posting. In your OP, you have the following which looks like a major problem waiting to happen:

  my $mw = MainWindow->new();
  ...
  our $mw = MainWindow->new;
  [download]