Thanks for the help. I ended up re-installing superuser and going to the titanium preferences and selecting auto, indirect, instead of auto, direct, and it works fine now. I dunno why mine has to be different than everyone else's but as long as it works I'm happy. I've been punching bloatware in the face left and right now it's awesome! Notes Mobile is by far the worst offender.. After I've killed all the apps I know are safe to remove I'll do a backup with cwm and start killing off the apps I'm not sure about.
The problem of USB debugging un-checking itself upon reboot persists though, and I don't think I did that before.