I believe you can do this with the MIDI Modifier section. On your MIDI track, click on MIDI Modifiers and mess around with the Note Filter settings. I believe you can set a low note and a high note, and it will filter out everything else. You should be able to filter out the low notes on one track, and the high notes on another.

Yes, using the MIDI Remote feature, you can set buttons on your midi device to skip to markers 1-9.

I would route each of the instruments to their own output in Kontakt, then use the bounce function. On the left if you select multi, you can then select each output of Kontakt and bounce them each to separate audio files and import them through there.