Short answer:

I've no idea

Long answer:

It depends. If problems were caused by speedpatch, maybe - I don't know how good post-uninstall scripts of speedpath are. I would rather try with full reflash, kp, CSSU without speedpath.

Anyway, I don't know what exactly is wrong with Your filesystem. It looks ok, doesn't it? If You mean lack of some folder - like Camera - maybe You've not get any photos, and appropriate folder was not created yet?