The MIDI notes are colored according to a
midi_note_colormap.png image which is inside the theme, so you could just swap this image with some other colormap. Or set your new colormap in Preferences/Editing Behavior/MIDI Editor -> Default note colormap. You can also load these colormap files from the MIDI editor File/Customize note colors menu. In these cases you'd have to have the new colormap images available somewhere separately to be able to browse to them.
Here's how midi_note_colormap images are constructed:
http://forum.cockos.com/showpost.php...20&postcount=2
And here are some custom ones people have offered:
https://stash.reaper.fm/browse.php?q=colormap&x=0&y=0
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edit: Blankfiles, I've been following the development of your I Logic theme and must say it looks nice and clear so far. Thanks for continuing with it.