apache http 80 .htacess, https 443 .htaccess does not work - apache

Question

When I run api.troop37bsa.org/user, I am able to access the page but when I run https://api.troop37bsa.org/user, I get a 404 error. When I run api.troop37bsa.org/?url=user or the secure version I get the correct page.
I am using a .htaccess file to rewrite the url so that everything after the subdomain is considered a parameter string.
So my question is two fold. How can I get https://api.troop37bsa.org/user to work and also what can I do to reduce the size of my .conf file and reduce or merge my .htaccess file.
I have an Apache Server 2.4.18.
My .conf file is setup as follows:
<VirtualHost *:80>
ServerAdmin kreichner#troop37bsa.org
ServerName api.troop37bsa.org
ServerAlias api.troop37bsa.org
DocumentRoot /var/www/troop37bsa.org/api/public
<Directory /var/www/troop37bsa.org/api/public>
DirectoryIndex index.php index.html
Options Indexes FollowSymLinks MultiViews
AllowOverride All
Order allow,deny
allow from all
# Uncomment this directive is you want to see apache2's
# default start page (in /apache2-default) when you go to /
#RedirectMatch ^/$ /apache2-default/
</Directory>
AccessFileName .htaccess
ErrorLog /var/www/troop37bsa.org/api/public/apache_error.log
CustomLog ${APACHE_LOG_DIR}/access.log combined
#RewriteEngine on
#RewriteCond %{SERVER_NAME} =api.troop37bsa.org
#RewriteRule ^ https://%{SERVER_NAME}%{REQUEST_URI} [END,QSA,R=permanent]
</VirtualHost>
<VirtualHost *:443>
ServerAdmin kreichner#troop37bsa.org
ServerName api.troop37bsa.org
ServerAlias api.troop37bsa.org
DocumentRoot /var/www/troop37bsa.org/api/public
<Directory /var/www/troop37bsa.org/api/public>
DirectoryIndex index.php index.html
Options Indexes FollowSymLinks
AllowOverride All
Order allow,deny
allow from all
# Uncomment this directive is you want to see apache2's
# default start page (in /apache2-default) when you go to /
#RedirectMatch ^/$ /apache2-default/
</Directory>
AccessFileName .htaccess
ErrorLog /var/www/troop37bsa.org/api/public/apache_https_error.log
CustomLog ${APACHE_LOG_DIR}/access.log combined
</VirtualHost>
In my subdomain folder (ie /var/www/troop37bsa.org/api/public) I have an .htaccess file
ReWriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond $0#%{REQUEST_URI} ([^#]*)#(.*)\1$
RewriteRule ^(.+)$ %2index.php?url=$1 [QSA,L]
I am also using a letsencrypt SSL certificate that otherwise seems to be working fine.
Thanks

Answer 1

As I said in the comment section, It turns out that there was a conf file generated by letsencrypt, but it was pointing to the wrong directory publicl instead of public. When I changed the directory name. the .htaccess file did its job. I also removed the second *.443 virtualHost from my orginal conf to avoid further conflicts.
So others may not fall into the same problem the name of the conf was api.troop37bsa.org-le-ssl.conf. This set up the look ups from the SSL certificate.
the api.troop37bsa.org-le-ssl.conf code is as follows:
<IfModule mod_ssl.c>
<VirtualHost *:443>
ServerAdmin kreichner#troop37bsa.org
ServerName api.troop37bsa.org
ServerAlias api.troop37bsa.org
DocumentRoot /var/www/troop37bsa.org/api/public
<Directory /var/www/troop37bsa.org/api/public>
Options Indexes FollowSymLinks MultiViews
AllowOverride All
Order allow,deny
allow from all
# Uncomment this directive is you want to see apache2's
# default start page (in /apache2-default) when you go to /
#RedirectMatch ^/$ /apache2-default/
</Directory>
ErrorLog ${APACHE_LOG_DIR}/error.log
CustomLog ${APACHE_LOG_DIR}/access.log combined
SSLCertificateFile /etc/letsencrypt/live/troop37bsa.org/fullchain.pem
SSLCertificateKeyFile /etc/letsencrypt/live/troop37bsa.org/privkey.pem
Include /etc/letsencrypt/options-ssl-apache.conf
</VirtualHost>
Thank you everyone for your help.