If you want to upgrade the LAMP components, you need to launch a new instance and migrate the data (database and app's files) from the old instance to the new one.
You can also stop the installation in your current instance and install the latest installer in the same instance but you will also need to migrate the data from one installation to the other one.
As I mentioned, you need to backup the database data and stop the installation before installing the new version. The cloud instances doesn't have the uninstaller file, you can simply stop the services and remove the folder.
Are you sure you are accessing the phpMyAdmin of the new installation or the one of the old one? You need to specify the Apache's port of the installation.
If you use the installer, you need to load the Bitnami's environment.
Sorry to hear that, but the easiest way to upgrade the Bitnami stack is by launching a new instance and migrating the data.
Let us know if you have any questions