hmmm. i think if u follow the right direction, it shouldn't went wrong. if i am you right now, i would flash back a ics stock rom as to ensure the bootloader is right, then flash a temporary cwm, get it from here then do the clear stuff like full wipe / clear cache. then use odin reflash the 4.1.2 rom again. if things goes right, your phone should running smoothly.
note : to make things clear, apps is ok to be restore. is just some system setting or data regarding the system shouldn't be restore. good luck!