clean (format or just delete) 2nd 3rd 4th partition. you can do it manually on pc or using modified updater-script. using updater-script maybe easier. check
http://www.freeyourandroid.com/guide/introdution_to_edify if you want to know about edify (updater-script language).
i make this script (yes it's not kernel mod, it just simple init.rc mod) just for proof of concept. everything is hard-coded make it not flexible. right now i started working to add script capabilities to boot process. like "init.d" but with additional features. with proper script it can be data2sd, a2sd, dual boot, temporary install theme, etc. i just hope have enough free time this week end so i can finish it.