Broken includes and cgis with Apache 2.4 update

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I have a site with the following .htaccess:

Options +ExecCGI +Includes
AddType text/html .shtml
AddOutputFilter INCLUDES .shtml
AddType application/x-httpd-cgi .cgi/
AddType application/x-httpd-cgi .pl
AddType application/x-httpd-cgi .pl/
AddType text/css .css

I also have Addtype and AddOutputFilter lines in the httpd.conf (in the ifmodule mime_module, as well as the following block:

<Directory "/usr/local/www">
 Options +Indexes +FollowSymLinks +Includes -SymLinksIfOwnerMatch
 AllowOverride All
 Require all granted
</Directory>

and on the index.shtml page I have

<div class=purple>
<!--#include file="menu.inc"-->
</div>

This all worked in apache 2.2 (with AddHandler server-parsed .shtml), but under 24 the menu.inc file is not
loading. Since the content of the site has not changed in 11 years, so this is definitely something I've missed in the Apache configuration for 2.4.

Also, none of the .pl files are being executed, instead just displaying their source.

# apachectl -M
Loaded Modules:
core_module (static)
so_module (static)
http_module (static)
mpm_prefork_module (static)
authn_file_module (shared)
authn_core_module (shared)
authz_host_module (shared)
authz_groupfile_module (shared)
authz_user_module (shared)
authz_core_module (shared)
access_compat_module (shared)
auth_basic_module (shared)
reqtimeout_module (shared)
include_module (shared)
filter_module (shared)
mime_module (shared)
log_config_module (shared)
env_module (shared)
mime_magic_module (shared)
headers_module (shared)
setenvif_module (shared)
version_module (shared)
unixd_module (shared)
dav_module (shared)
status_module (shared)
autoindex_module (shared)
info_module (shared)
cgi_module (shared)
dav_fs_module (shared)
vhost_alias_module (shared)
dir_module (shared)
userdir_module (shared)
alias_module (shared)
rewrite_module (shared)
php5_module (shared)
# apachectl -V
Server version: Apache/2.4.6 (FreeBSD)
Server built:   Aug  3 2013 19:16:24
Server's Module Magic Number: 20120211:23
Server loaded:  APR 1.4.8, APR-UTIL 1.5.2
Compiled using: APR 1.4.8, APR-UTIL 1.5.2
Architecture:   64-bit
Server MPM:     prefork
threaded:     no
 forked:     yes (variable process count)
Server compiled with....
-D APR_HAS_SENDFILE
-D APR_HAS_MMAP
-D APR_HAVE_IPV6 (IPv4-mapped addresses enabled)
-D APR_USE_FLOCK_SERIALIZE
-D APR_USE_PTHREAD_SERIALIZE
-D SINGLE_LISTEN_UNSERIALIZED_ACCEPT
-D APR_HAS_OTHER_CHILD
-D AP_HAVE_RELIABLE_PIPED_LOGS
-D DYNAMIC_MODULE_LIMIT=256
-D HTTPD_ROOT="/usr/local"
-D SUEXEC_BIN="/usr/local/bin/suexec"
-D DEFAULT_PIDLOG="/var/run/httpd.pid"
-D DEFAULT_SCOREBOARD="logs/apache_runtime_status"
-D DEFAULT_ERRORLOG="logs/error_log"
-D AP_TYPES_CONFIG_FILE="etc/apache24/mime.types"
-D SERVER_CONFIG_FILE="etc/apache24/httpd.conf"
# apachectl -t
Syntax OK


-- 
'Where's the gritsucker? And the rock?' 'Ah,' said Vimes, 'you are
referring to those representative members of our fellow sapient races
who have chosen to throw in their lots with the people of this city?' 'I
mean the dwarf and the troll,' said Quirke. --Men at Arms


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