Yes, that is really a mess!
Or nicely stacked, as juiceme would say.

You somehow managed to shift roots and home from p2/3 to p3/4.
Your approach above editing ubiboot.conf may work (for sure this is the reason why kernels are not found), as it searches on harmattan rootfs (i.e. /dev/mmcblk0p2) boot folder. But due to your partition layout they reside on /dev/mmcblk0p4.

I suggest you do a reflash --no-preserve and start all over.
But before you should try editing ubiboot.conf as stated above.
And you will end up with a system having the home partition not mounted (would need editing at least /etc/fstab). Juiceme may tell more here.

--
did you ever try to flash standard open mode kernel and see how the N9 behaves?