You're basically holding a discussion with yourself here, but - you only ever directly download & install XCode from the one and only verified source there is: Apple.
If you did download your copy from Apple, there isn't any reason not to follow through with the installation.
The items disappearing from the Utility pane - I've had that since seemingly ever. It is irritating, but always remedied easily by switching between open files or at worst restearting XCode.
Your other issues are hard to follow, given you mix them all up over various posts.
"Things" persisting in test apps where they shouldn't are usually avoided by:
- Clean Project
- Clean Build Folder
- Clear the content of the "Derived Data" Folder
Also if you've downloaded XCode and it only has 344kb then you know you haven't downloaded XCode.
Last but not least - are your added subviews "deleted" in Interface Builder or are not not visible?
My guess is - not visible (which basically is the thread where you came from).
So - are they visible in the document outline (the column left of your Interface Builder where all document elements are listed in a hierarchical view) or not?
If so, they're not deleted.