4) I can't seem to figure out how to save audio settings such that pd starts up JACK and ALSA MIDI upon startup. Every time I start it, I have to manually go into the Media menu, and select JACK, and tell it how many audio ports (it doesn't remember), and select the ALSA-MIDI dialog box and tell it how many MIDI ports (it *does* remember that), before it opens the ALSA port. I'd like both to happen automatically at startup. I'm using "pd -rt -jack -alsamidi" but it seems to disregard those.

In Montreal I was having a problem like this, and with a little help from Iohannes, found that the following arguments worked for me:

# start jack
jackd -d alsa -d hw:0 -r 44100 -p 512

# start pd
pd -jack -audiodev 0 -channels 2

(without the "-channels 2" flag, it would segfault, and without the "-audiodev 0" flag it would ignore the -jack flag)

I just tried this, and it did what you're trying to do:
pd -jack -audiodev 0 -channels 2 -alsamidi

hope that helps,
-David M.