MainLoop started in script #1. Also, script #1 has a button, "Start #2".

Transform script #2 into a "standalone" widget, something like:

package Widget2;

Construct Tk::Widget 'Widget2';

use Tk;
use Tk::Frame;

# go ahead and create elements in the widget, like it would be a 
# standalone app (don't forget to add the close button :D
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Somewhere in #1 you have ...

sub load_tool {
    my $class = shift;
    my $wdg_plugin;    #plugin's own widget
    eval {
        require $class . ".pm";

        if ( "$class"->isa("Tk::Widget") ) {

            #If there is a UI then load as widget
            $wdg_plugin = $mw->$class(    #we're sending references
            )->pack();
        }
    };

    #if any errors occurred, report them
    if ($@) {
        my $msg = "Initialization of tool $class failed:\n\n";
    }
}
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I hope you got the idea ...