Damn, you went all out with the cod files, did you follow john clark's instructions, because i didn't see him mentioning any of those files except for themes and other apps such as bbmaps, ppt, voice dialing.
Technically, you aren't supposed to delete them. You are supposed to move them to a new folder. That way if you screw something up, like you did, you can simply move those files back. Try reinstalling the OS software on your computer again.
Only difference from deleting and moving to another folder is that if you delete it, its gone permantly. Regardless, as long as its out of the java folder you would have gotten the same error, best thing to do would be to uninstall the device software from your comp, reinstall it and then delete/move cod files that were suggested from john clark and then run the apploader again. If you want to get rid of more cod files, do them one at a time and see which one causes the error.