Re: problems with home directory
By default no system files go into your home directory at all. It sounds to me like you had some files owned by root in your home directory (which can happen if you run programs as root and they create config files). I don't think an upgrade from Gutsy to Hardy touches a single file in your home directory but, upgraded apps may want to modify config files after they are started the first time. If those files were owned by root, it would cause the kinds of problems you are describing.
Don't try to make something "fast" until you are able to quantify "slow".