Looking at that circuit again, I don't think that tying all the +5V pins together is a good idea. It's definitely not necessary for the power switching circuit, and your Amiga won't need that much current either. These pins could be connected to separate +5V outputs from within the power supply and are supposed to supply several amps each (IIRC). Any disparity in +5V from any of these will cause currents to flow between the multiple +5V outputs. At the bare minimum, it's a waste of power.
Hans