So I wouldn't worry about downloading and uploading config.php and plugin folders. It is much easier and will retain permissions correctly if you just copy the needed files and folders over from your moodleold folder. (This might have been your issue - permissions might not have been quite right on some things that you added back in) Checking your plugins page for additional plugins will give you a nice list of all plugins that you have added so that you can make sure that you get them all.
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