Create a brand new save on your PS3. Just select new game and allow it to create a new save right off the bat and quit the game, make sure it saves in the first slot if you're on 3.55 CFW. Use the PARAM.SFO from new game save you created in the tool resigner from this thread,
http://www.ps3hax.net/showthread.php?t=48862 , on the right tab load your PARAM.SFO, save as profile 1, 2, or 3, make sure you have the public keys entered, saved, and put the Secure ID in the games.conf. I didn't need the console ID when I resigned. Load the save you want to resign from the left tab. Select the profile from the drop down list, hit resign. Copy it back via the XMB and overwrite the save. I noticed in your post how you said stage 2 saves never finish. This is a problem with 3.55 CFW and FFXIII-2, it only allows you to use save slot one because of the auto save function. It doesn't save properly in other slots. That's why saves in slot 2 ,3,4, ect., never finish saving stage 2 and 3, and will replay the stage when you load them. If you upgrade to Rogero 4.30 this problem is fixed.