Nice analysis - powering up devices in an appropriate order can definitely cause problems such as via the (parasitic) static protection diodes seen on various pins. Presumably this invokes Yveaux's interest in current limiting resistors.
It's a bit unclear how the layout under discussion is actually powered. A cct diagram would be useful here but generally speaking, everything should be powered up pretty much simultaneously, if possible. Regardless the various arduino ccts in existence seem to provide a variety of power paths, many of which are perhaps undesirable. eg supplying power directly to power lines that have on board regulators and hoping that "back driving" those regulators will not cause problems. Likewise various arduinos use the serial chip to provide some power and it's quickly overloaded.
A detailed cct is required to provide any definitive PSU analysis.