This is untested, but may be a good start:

#!/usr/bin/perl
my $top2 = MainWindow->new();
my $waitbox = $top2->WaitBox(-title=>"Connecting to agent $port",
        -txt1=>"Connecting to  Agent $port.\nConnection will be establ
+ished when this box closes.\n",
        -cancelroutine=>sub {
            print "\nCancelling...\n";
            $top2->unShow;
            die}
        );
# pack the widgets

$waitbox->pack;

# encapsulate the wait box posting
# and the connect routine in a sub
# ( the waitbox is just using a "grab" and "focus",
#    if you want to roll your own, see Tk::Grab )
sub doyourstuff { 
   # post the waitbox, this doesn't block
   # the process, it just grabs all the keyboard
   # and mouse events and discards them for a while
   $waitbox->Show;
   # do your connect stuff here
   for (1..10)  {
        print STDERR "waiting $_\n";
        sleep(1);
   }
   # get rid of the waitbox and start taking mouse/kb
   # events again.
   $waitbox->unShow;
}
# schedule the doyourstuff subroutine to 
# run in 0 ms
$top2->after(0,\&doyourstuff);
MainLoop();
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