After looking everything over, I think I’m gonna use Wiering’s base code that he posted up, built on haXe. So my final list should be:

Wiering’s boilerplate: http://www.wieringsoftware.eu/

haXe + FlashDevelop + SWFMill

Tile Studio (which I have absolutely fallen in love with), Gimp, Wacom Tablet

My Tenori-On, Korg KP3, Audacity, and likely sfxr.