[Android Q&A, Help & Troubleshooting] shimp208:
After taking a look at your two updater-script files, I noticed that you had copied your mod's updater-script file contents into the end of your rom's updater-script file. One of the reasons your mod file wasn't working in your rom script is because the mod script was unmounting the /system directory before modifications could be made and also it was extracting the /system directory contents when it had already previously extracted the /system directories contents. Also make sure that in your ROM's .zip file that the contents of the Mod's .zip are also included (For example if your Mod includes files in the /system/app directory make sure your ROM's .zip file has those same files in the /system/app directory etc.). Below is an modified updater-script for your ROM that includes the Mod's script contents the changes that were made from the original ROM updater-script are in red:

show_progress(0.1, 0);
unmount("/system");
format("ext4", "EMMC", "/dev/block/mmcblk0p14", "0");
mount("ext4", "EMMC", "/dev/block/mmcblk0p14", "/system");
package_extract_dir("system", "/system");
symlink("dumpstate", "/system/bin/dumpcrash");
symlink("toolbox", "/system/bin/cat");
symlink("toolbox", "/system/bin/chmod");
symlink("toolbox", "/system/bin/chown");
symlink("toolbox", "/system/bin/cmp");
symlink("debuggerd", "/system/bin/csview");
symlink("toolbox", "/system/bin/date");
symlink("toolbox", "/system/bin/dd");
symlink("toolbox", "/system/bin/df");
symlink("toolbox", "/system/bin/dmesg");
symlink("toolbox", "/system/bin/getevent");
symlink("toolbox", "/system/bin/getprop");
symlink("toolbox", "/system/bin/hd");
symlink("toolbox", "/system/bin/id");
symlink("toolbox", "/system/bin/ifconfig");
symlink("toolbox", "/system/bin/iftop");
symlink("toolbox", "/system/bin/insmod");
symlink("toolbox", "/system/bin/ioctl");
symlink("toolbox", "/system/bin/ionice");
symlink("toolbox", "/system/bin/kill");
symlink("toolbox", "/system/bin/ln");
symlink("toolbox", "/system/bin/log");
symlink("toolbox", "/system/bin/ls");
symlink("toolbox", "/system/bin/lsmod");
symlink("toolbox", "/system/bin/lsof");
symlink("toolbox", "/system/bin/mkdir");
symlink("toolbox", "/system/bin/mount");
symlink("toolbox", "/system/bin/mv");
symlink("toolbox", "/system/bin/nandread");
symlink("toolbox", "/system/bin/netstat");
symlink("toolbox", "/system/bin/newfs_msdos");
symlink("toolbox", "/system/bin/notify");
symlink("toolbox", "/system/bin/printenv");
symlink("toolbox", "/system/bin/ps");
symlink("toolbox", "/system/bin/reboot");
symlink("toolbox", "/system/bin/renice");
symlink("toolbox", "/system/bin/rm");
symlink("toolbox", "/system/bin/rmdir");
symlink("toolbox", "/system/bin/rmmod");
symlink("toolbox", "/system/bin/route");
symlink("toolbox", "/system/bin/schedtop");
symlink("toolbox", "/system/bin/sendevent");
symlink("toolbox", "/system/bin/setconsole");
symlink("toolbox", "/system/bin/setprop");
symlink("mksh", "/system/bin/sh");
symlink("toolbox", "/system/bin/sleep");
symlink("toolbox", "/system/bin/smd");
symlink("toolbox", "/system/bin/start");
symlink("toolbox", "/system/bin/stop");
symlink("toolbox", "/system/bin/sync");
symlink("toolbox", "/system/bin/top");
symlink("toolbox", "/system/bin/touch");
symlink("toolbox", "/system/bin/umount");
symlink("toolbox", "/system/bin/uptime");
symlink("toolbox", "/system/bin/vmstat");
symlink("toolbox", "/system/bin/watchprops");
symlink("toolbox", "/system/bin/wipe");
symlink("toolbox", "/system/bin/chcon");
symlink("toolbox", "/system/bin/setenforce");
symlink("toolbox", "/system/bin/grep");
symlink("toolbox", "/system/bin/runcon");
symlink("toolbox", "/system/bin/touchinput");
symlink("toolbox", "/system/bin/md5");
symlink("toolbox", "/system/bin/getsebool");
symlink("toolbox", "/system/bin/setsebool");
symlink("toolbox", "/system/bin/restorecon");
symlink("toolbox", "/system/bin/getenforce");
symlink("toolbox", "/system/bin/load_policy");
symlink("toolbox", "/system/bin/cp");
symlink("toolbox", "/system/bin/playback");
symlink("toolbox", "/system/bin/du");
symlink("wiperiface_v02", "/system/bin/wiperiface");
set_perm_recursive(0, 0, 0755, 0644, "/system");
set_perm_recursive(0, 2000, 0755, 0755, "/system/bin");
set_perm(0, 3003, 06755, "/system/bin/ip");
set_perm(0, 3003, 02750, "/system/bin/netcfg");
set_perm(0, 3004, 02755, "/system/bin/ping");
set_perm(0, 2000, 06750, "/system/bin/run-as");
set_perm_recursive(1002, 1002, 0755, 0440, "/system/etc/bluetooth");
set_perm(0, 0, 0755, "/system/etc/bluetooth");
set_perm(1000, 1000, 0640, "/system/etc/bluetooth/auto_pairing.conf");
set_perm(3002, 3002, 0444, "/system/etc/bluetooth/blacklist.conf");
set_perm(1002, 1002, 0440, "/system/etc/dbus.conf");
set_perm(1014, 2000, 0550, "/system/etc/dhcpcd/dhcpcd-run-hooks");
set_perm(0, 2000, 0550, "/system/etc/init.goldfish.sh");
set_perm_recursive(0, 0, 0755, 0555, "/system/etc/ppp");
set_perm_recursive(0, 2000, 0755, 0644, "/system/vendor");
set_perm_recursive(0, 0, 0755, 0644, "/system/vendor/firmware");
set_perm(0, 2000, 0755, "/system/vendor/firmware");
set_perm(0, 2000, 0755, "/system/vendor/lib");
set_perm(0, 2000, 0755, "/system/vendor/lib/hw");
set_perm_recursive(0, 2000, 0755, 0755, "/system/xbin");
set_perm(0, 1000, 0755, "/system/xbin/busybox");
symlink("/system/xbin/busybox", "/system/bin/busybox");
run_program("/system/xbin/busybox", "--install", "-s", "/system/xbin");
set_perm(0, 0, 06755, "/system/xbin/su");
symlink("/system/xbin/su", "/system/bin/su");
show_progress(0.1, 10);
show_progress(0.2, 0);
[B][COLOR="Red"]mount("ext4", "EMMC", "/dev/block/mmcblk0p12", "/data");
delete_recursive("/data/dalvik-cache");
mount("ext4", "EMMC", "/dev/block/mmcblk0p8", "/cache");
delete_recursive("/cache");
delete("/system/app/SystemUI.apk");
delete("/system/app/SecLauncher.apk");
delete("/system/app/SecPhone.apk");
delete("/system/app/3Minit_Settings.apk");
delete("/system/app/LidroidSettings.apk");
delete("/system/framework/android.policy.jar");
delete("/system/framework/framework-res.apk");
delete("/system/framework/lidroid-res.apk");
set_perm_recursive(0, 0, 0755, 0644, "/system/framework");
set_perm_recursive(0, 0, 0755, 0644, "/system/app");[/COLOR][/B]
package_extract_file("boot.img", "/dev/block/mmcblk0p7");
show_progress(0.2, 10);
unmount("/system");

The code above is a suggestion for what you may want to try to get the Mod working in your ROM's updater-script.