I tried the v2 script in the first link in you post. I had to comment out the firmware checking as it's still for PR1.2.
M32GBinit.sh ran as before. I let the phone to finish the job and just checked to see if it's done a couple of times.
Then suddenly the phone reboot itself, and ran into sorta infinite loops:
dim nokia screen => five dots flahsed a couple of sec => reboot again
Then I reflashed the stock PR1.3 and the phone boot up again. What's interesting is my desktop and other personal settings are set back to default. Files under /home and /MyDocs and contacts are intact, including the directories copied by the script.
df -h /root showed the rootfs was in the factory state.
I am not sure if it has to do with kernel-power or overclocking (@1GHz constantly). fbcon.so is not there, but i have yet to add it to the modules. Doesn't it matter if the kernel(-power) is newer than the modules (fbcon for stock PR1.2)?
I will try again when things are clearer.

PS I won't use R&D mode. Just want to have enough space to set up a compilation environment.