So you now have full root access to your hosting right? Do you have write permissions one level above your public_html folder? If so, move your .env file, config & vendor folders one level above your web root.
You shouldn’t have to follow those instructions. have a look a the Bedrock documentation: https://roots.io/bedrock/docs/folder-structure/
No need to do that either, change it back to default:
require(__DIR__ . '/wp/wp-blog-header.php');
Also not necessary, change it back to default:
Treat your local Bedrock web folder as the remote public_html folder on your VPS.
$webroot_dir path in config/application.php and replace web so it matches your root folder name (public_html, httpdocs etc)
That should basically be it.