WS Rom/KToonsez Kernel/Philz Touch Recovery(CWM).. topic

Hey all, I posted this in the Q&A section but didn't get any response so I thought I would try here. I have a Sprint GS3 rooted running Philz Touch recovery, Wicked Sensations Rom, and KToonsez Kernel. I did clean flashes when I did each one only when I installed the KToonsez kernel I didn't know how to "fix permissions" and I also didn't know how to go in and "stop mpdecision from being called". I seem to be having a few glitches, nothing too serious but glitches none the less. I'm wanting to do a re-flash of Philz Touch recovery, a re-flash of WS Rom, and re-flash of KToonsez kernel. I'm changing my SD card for a new/bigger one, my question is what would be the best order of re-flashing?, and could someone tell me how to fix permissions and stop mpdecision from being called? Also what benefit would I get from formatting the internel storage and such? Thanks for reading and thanks in advance for your help...Phil