Before deleting any keys, when you reach the startupreg key, choose File > Export from Registry Editors menu and save the file to your desktop (just for safety purposes. I've never had a problem doing this, but if you inadvertently delete something you want back, you have a copy of the key before any changes are made.
To remove all those unchecked boxes under msconfig, (and there may be many) you can get rid of them using the Registry Editor.
Assuming you will never activate these entries again, go to Start > Run, and type regedit.
Navigate to HKEY_LOCAL_MACHINE, scroll down to the Software key, scroll down to the Microsoft key, scroll down to Shared Tools, scroll down to msconfig, click the stratupreg key and delete the entries you'll never activate again. The entries will not show up the next time you run msconfig.