I figured out a sort of work around. As far as I can tell, the Control, Shift, and Alt keys all work they way I'd like my other keys to work (only one KeyPress/KeyRelease). I used that to do this:

$top->bind('<Control-KP_Left>'  => sub{ &pressed("left",1,2) });
$top->bind('<Control-KP_Down>'  => sub{ &pressed("back",0, 7) });
$top->bind('<Control-KP_Right>' => sub{ &pressed("right",5, 6) });
$top->bind('<Control-KP_Home>'  => sub{ &pressed("spinl",1, 3, 5, 7) }
+);
$top->bind('<Control-KP_Up>'    => sub{ &pressed("forward",3, 4) });
$top->bind('<Control-KP_Prior>' => sub{ &pressed("spinr",0, 2, 4, 6) }
+);

sub pressed
{
    my @args = @_;
    my $arg  = shift @args;
    &fire_thrusters(@args);
    for ($arg){
    /left/i    && do { $top->bind('<Control-KP_Left>'  => sub{}); };
    /right/i   && do { $top->bind('<Control-KP_Right>' => sub{}); };
    /back/i    && do { $top->bind('<Control-KP_Down>'  => sub{}); };
    /forward/i && do { $top->bind('<Control-KP_Up>'    => sub{}); };
    /spinl/i   && do { $top->bind('<Control-KP_Home>'  => sub{}); };
    /spinr/i   && do { $top->bind('<Control-KP_Prior>' => sub{}); }; 
    }
    $top->bind('<KeyRelease-Control_R>' => sub{ &released($arg) });
    $top->bind('<KeyRelease-Control_L>' => sub{ &released($arg) });
}

sub released
{
    my $arg = shift;
    &stop;
    for ($arg){
    /left/i    && do { $top->bind('<Control-KP_Left>'  => sub{ &presse
+d("left",1,2) }); };
    /right/i   && do { $top->bind('<Control-KP_Right>' => sub{ &presse
+d("right",5, 6) }); };
    /back/i    && do { $top->bind('<Control-KP_Down>'  => sub{ &presse
+d("back",0, 7) }); };
    /forward/i && do { $top->bind('<Control-KP_Up>'    => sub{ &presse
+d("forward",3, 4) }); };
    /spinl/i   && do { $top->bind('<Control-KP_Home>'  => sub{ &presse
+d("spinl",1, 3, 5, 7) }); };
    /spinr/i   && do { $top->bind('<Control-KP_Prior>' => sub{ &presse
+d("spinr",0, 2, 4, 6) }); };
    }
    $top->bind('<KeyRelease-Control_R>' => sub{});
    $top->bind('<KeyRelease-Control_L>' => sub{});
}
[download]

Now the user can press Ctrl-8 and hold Ctrl until they want to call the &released function. It's not nearly as cool as just holding down the Numpad keys, but I guess it'll work. If someone has a better solution please post.