I am glad it's working for you. The modification isn't something I am going to release as an update, since it breaks the resetting of the 'S'M'R' button lights. I will post it here for others though in case its useful to anyone else.
you can use the Korg Nano Kontrol Editor software to assign different control numbers to each unit if you want to keep them both on the same port/channel. or assign different channels or ports. free download here
i know what midi messages the Kaoss DJ sends (it's in the manual, mostly control and note-on). other midi controllers I use (arturia mini lab) work out of the box.
it must be related to Korg using a different MIDI implementation.