Hi!
Sorry, been a while since I followed this thread, sorry for this late reply!
It should be quite easy to use my firmware version with your own project. Just do as follows. If this does not work, let me know what problem you encounter and I'll see if I forgot something:
1) I'm assuming you have a working devKitPro installation, with a recent devKitPro version. If not, set it up. :-)
2) Download http://dsx86.patrickaalto.com/ds2_firmware.zip from my dsx86 pages.
3) Extract ds2_firmware.zip to some suitable folder. It includes a ready-built ds2_firmware.dat, so you can skip the next step if needed.
4) Build ds2_firmware.dat from the sources in my zip.
5) Back up your current ds2sdk_r/tools/ds2_firmware.dat
6) Copy my ds2_firmware.dat to ds2sdk_r/tools directory.
7) Build your DSTwo homebrew software.
8) Test your DSTwo homebrew software. The graphics should work, but as I did not add audio support to my firmware, you won't get audio. There are also other features missing, like the ability to launch other plugins, or the ability to return to DSTwo menu.
If you get that far without problems, feel free to edit/enhance the NDS side so it includes audio and whatever features you need. :-)
Pate