Okay, just read logs again.
And it is really like the kernel gets loaded but then dies out. So it is not ubiboot boot sequence causing this mess.

i do not understand the p3 (/home) thing. If this is true, then you are out of luck to ever get Nitdroid running. Or you pack it on another partition and modify the /sbin/preinit_nitdroid script .....

... Ah maybe it is an easy and now remembered often made mistake:
Please check the exec rights of the file /sbin/preinit_nitdroid under booted Harmattan via ls -l /sbin/preinit_nitdroid (should be: rwxr-xr-x).
If it misses the exec bits, do chmod +x /sbin/preinit_nitdroid (under devel-su).

If that does not help you have to wait for juiceme (as he is much better in reading his logs ).
Or you may connect your powered off N9 via USB to a PC (flavour Linux), then you possibly might find out why p3 is not mounted...