I had a problem with my iPhone recently and had some success with iLex R.A.T. There are several settings for wiping things out including a full reset (which I did) I think it removed 99% of everything and the phone started as if after an iTunes restore, but with your jailbreak intact. You need to add the repo to Cydia and go from there... Not promoting one way or another, just suggesting what worked for me.
Could someone explain this a bit more? I'm getting tired of my jailbroken phone always crashing and I think I want to start over. My phone crashes FB and the Camera the most and it's annoying..I think starting over my be my best option.
Uninstall mobile substrate and all of your tweaks wil bel uninstalled, than to install other tweaks, you will have to install mobile substrate again. Uninstalling mobile substrate is easier because you don't have to manually remove every tweak.And to remove the rest of the files, let's call them "left overs" that the tweaks leaves them on os, use icleaner, it deletes safari cache, file type clean up, temporally files, cache files,log files, unused dependencies, and files from app store apps that failed to install or are half installed, probably after a ba sync with iTunes. I don't think I am allowed to write the repo where you can find icleaner pro but you can google it, there is already an"icleaner" in Cydia but that is not that good. Good luck