At the moment the MIDI commands will be played out of the Apple IIe by just sending the MIDI data out of the Super Serial Card. The Arduino will simply repeat the same data out of its attached MIDI port at the correct baud rate.
Music will be composed on a normal sequencer and saved to a MIDI file. The MIDI file will then be converted to a CSV file (with http://www.fourmilab.ch/webtools/midicsv/#Download) that can be easily converted to an Applesoft BASIC program in DATA statements.
I'm not sure how stable timing will be, but we'll find out.
Next steps would be to get an Apple analogue joystick, and use that to control the Moog's filter. Also to build a bit more of a suitably flashy vintage on-screen display.