The "normal" setting for files is 644, that allows anyone to read the file, but only the owner can write to it. For php files the execute flag doesn't matter. That setting should also allow you to do the site transfer, assuming that your ftp user and your web user are the same (that is not always true). When the users are not the same, you generally use ftp mode within Joomla! so that all of your files are owned by the ftp user.
I prefer to delete all the files on the site before restoring. I also manually drop the tables. That is just personal preference. In theory, all of the tables will be dropped and replaced and all of the files will be overwritten. That's one reason you don't overwrite different versions, the files won't all be overwritten and you will leave orphan files on your site. They generally don't do any harm, but they take up space on the site and in the backup. If you install a new component on your site, then overwrite it with a backup, those new files (and any tables added) will be orphaned. They will just sit there taking up space.
Dale
Dale L. Brackin
Support Specialist
English: native
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!
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My time zone is
EST (UTC -5) (click here to see my current time in Philadelphia, PA)