Its worth pointing out here, some of the files you have in locations have never actually been there. So its more than just leaving traces there.
You could certainly do it the way you have done there. However personally, if it were me I would have gone about it by sorting out your 4.x installation first. To do that, you would do the following
Delete everything other than
- Uploads Folder
-conf_global.php
- constants.php (if you have it)
- plugins folder
Upload a fresh set of files from your client area
Its important to note the following
This doesnt take into account any 3rd party applications you may have in your applications folder. If you do have any, copy those folders out, and re-add them to your uploads folder once the above is done
It assumes all storage locations are in the default 'uploads' location. You would need to adjust your steps accordingly if you have changed these