Issues with aliases and errors on various self hosted apps

I have a VPS running CentOS 7, and I'm having some trouble with a few pieces of software that I'm trying to run. My miniflux instance is working, but all the other software I'm trying to setup with aliases is not working. I know the config is a mess as I've just copy and pasted from various install documentations. I've read the documentation but I'm still having some issues.

Errors

Misc:

directive "index" is not terminated by ";" in /etc/nginx/sites-enabled/mysite.conf:54

Not sure why as index.php is followed by a semicolon

mysite.tld/budget (firefly-iii):

FastCGI sent in stderr: "Access to the script '/var/www/mysite/firefly-iii/public/index.php/login' has been denied (see security.limit_extensions)" while reading response header from upstream, client: myip, server: mysite.tld, request: "GET /budget/login HTTP/1.1", upstream: "fastcgi://unix:/var/run/php-fpm/php-fpm.sock:", host: "www.mysite.tld"

Not sure how to get around this without disabling security.limit_extensions which seems to be a bad idea

mysite.tld/walla (Wallabag):

FastCGI sent in stderr: "Unable to open primary script: /var/www/mysite/app.php (No such file or directory)" while reading response header from upstream, client: 24.246.175.35, server: drewski.xyz, request: "GET /walla HTTP/1.1", upstream: "fastcgi://unix:/var/run/php-fpm/php-fpm.sock:", host: "www.mysite.tld"

For some reason it's trying to find app.php in the wrong folder

mysite.tld/wiki (Bookstack):

directory index of "/var/www/drewski.xyz/BookStack/public" is forbidden, client: myip, server: mysite.tld, request: "GET /wiki/ HTTP/1.1", host: "www.mysite.tld"

It's trying to list the directory index here instead of the index.php file for some reason

Here is my nginx config (with a few identifying infos changed):

https://pastebin.com/AztSysHv