You can add your new rule in the end:
RewriteEngine On
RewriteCond %{REQUEST_URI} ^(.*)//(.*)$
RewriteRule . %1/%2 [R=301,L]
RewriteRule ^(.*),(.*)$ $2.php?rewrite_params=$1&page_url=$2 [L,QSA]
RewriteCond %{QUERY_STRING} base64_encode.*(.*) [OR]
RewriteCond %{QUERY_STRING} (<|%3C).*script.*(>|%3E) [NC,OR]
RewriteCond %{QUERY_STRING} GLOBALS(=|[|%[0-9A-Z]{0,2}) [OR]
RewriteCond %{QUERY_STRING} _REQUEST(=|[|%[0-9A-Z]{0,2})
RewriteRule ^(.*)$ index.php [F,L]
RewriteRule ^stores/([0-9a-z.-]+)/?$ shop.php?shop_id=$1 [L,QSA,NC]