How about making the launcher buttons independent items on the Home? That way the application would require much simpler configuration UI. This is how it could work:
1 user checks the apps she wants to use on the settings dialog
2 user accepts the dialog
3 layout mode opens with all selected items
4 user can position them anywhere she wants or remove those buttons she doesn't
5 user accepts the layout

Also I would make the button by default a bit bigger so that you can tap them with finger, say something like 6-7 mm per dimension. Maybe an option is needed if someone wants to make them really small, by I'd expect most of people would be satisfied with one size.