Reinstalling won't change settings, what you need to do is make sure that the settings match the actual locations of the files. Make a list of which folders contain Runtime and/or data folders - those are probably your actual content directories (make sure you don't have one listed folder inside another) - the main exception being all the Connect folders, if anything was installed that way, where you want the folder that holds the /data/cloud/ folder not the /data/cloud/1_xxxxx/ folder that holds each product's own Data and Runtime folders.

Once you have the list you need to go to Edit>Preferences, then the Content tab within that, then click Content Directory Manager - there you can add, remove, and edit folders as needed.