Is there a way to auto set the midi preferences to, say, the IAC bus, when a patch is opened, or even when PD is opened? Currently I have to set it every time I open pd.

check out the startupflags:
http://en.flossmanuals.net/PureData/AdvancedConfig

i guess , you could get this to work using "-midiindev" / "-midioutdev"!?

THANK YOU SO MUCH!! It works!