[HD2 Android Q&A, Help & Troubleshooting and Genera] HypoTurtle:
Not to jinx it but the match should be a cakewalk.

Yea there's sed stuff that I thought was causing it (serach pattern having to be at least two lines, ignoring () and ;'s as they're special characters etc.), but can't find a reason.

I only tested the expression used initially with the symlink line and as it was working fine just used it for the rest.

What I've changed is that I removed the ( as it's being ignored anyway, and adding the ^ seems to have cut down most of the erroneous stuff.

Just so you can see:

cat $ups | sed -e '/^symlink/,/);/!d' gives you

symlink("../xbin/su", "/system/bin/su");
symlink("Roboto-Bold.ttf", "/system/fonts/DroidSans-Bold.ttf");
symlink("Roboto-Regular.ttf", "/system/fonts/DroidSans.ttf");
symlink("busybox", "/system/xbin/[", "/system/xbin/[[",
"/system/xbin/adjtimex", "/system/xbin/arp", "/system/xbin/ash",
"/system/xbin/awk", "/system/xbin/base64", "/system/xbin/basename",
"/system/xbin/bbconfig", "/system/xbin/blkid", "/system/xbin/blockdev",
"/system/xbin/brctl", "/system/xbin/bunzip2", "/system/xbin/bzcat",
"/system/xbin/bzip2", "/system/xbin/cal", "/system/xbin/cat",
"/system/xbin/catv", "/system/xbin/chattr", "/system/xbin/chgrp",
"/system/xbin/chmod", "/system/xbin/chown", "/system/xbin/chroot",
"/system/xbin/clear", "/system/xbin/cmp", "/system/xbin/comm",
"/system/xbin/cp", "/system/xbin/cpio", "/system/xbin/crond",
"/system/xbin/crontab", "/system/xbin/cut", "/system/xbin/date",
"/system/xbin/dc", "/system/xbin/dd", "/system/xbin/depmod",
"/system/xbin/devmem", "/system/xbin/df", "/system/xbin/diff",
"/system/xbin/dirname", "/system/xbin/dmesg", "/system/xbin/dnsd",
"/system/xbin/dos2unix", "/system/xbin/du", "/system/xbin/echo",
"/system/xbin/ed", "/system/xbin/egrep", "/system/xbin/env",
"/system/xbin/expand", "/system/xbin/expr", "/system/xbin/false",
"/system/xbin/fbsplash", "/system/xbin/fdisk", "/system/xbin/fgrep",
"/system/xbin/find", "/system/xbin/flash_lock",
"/system/xbin/flash_unlock", "/system/xbin/flashcp",
"/system/xbin/flock", "/system/xbin/fold", "/system/xbin/free",
"/system/xbin/freeramdisk", "/system/xbin/fstrim", "/system/xbin/fsync",
"/system/xbin/ftpget", "/system/xbin/ftpput", "/system/xbin/fuser",
"/system/xbin/getopt", "/system/xbin/grep", "/system/xbin/groups",
"/system/xbin/gunzip", "/system/xbin/gzip", "/system/xbin/halt",
"/system/xbin/head", "/system/xbin/hexdump", "/system/xbin/id",
"/system/xbin/ifconfig", "/system/xbin/inetd", "/system/xbin/insmod",
"/system/xbin/install", "/system/xbin/ionice", "/system/xbin/iostat",
"/system/xbin/ip", "/system/xbin/kill", "/system/xbin/killall",
"/system/xbin/killall5", "/system/xbin/less", "/system/xbin/ln",
"/system/xbin/losetup", "/system/xbin/ls", "/system/xbin/lsattr",
"/system/xbin/lsmod", "/system/xbin/lsusb", "/system/xbin/lzcat",
"/system/xbin/lzma", "/system/xbin/lzop", "/system/xbin/lzopcat",
"/system/xbin/man", "/system/xbin/md5sum", "/system/xbin/mesg",
"/system/xbin/mkdir", "/system/xbin/mke2fs", "/system/xbin/mkfifo",
"/system/xbin/mkfs.ext2", "/system/xbin/mkfs.vfat",
"/system/xbin/mknod", "/system/xbin/mkswap", "/system/xbin/mktemp",
"/system/xbin/modinfo", "/system/xbin/modprobe", "/system/xbin/more",
"/system/xbin/mount", "/system/xbin/mountpoint", "/system/xbin/mpstat",
"/system/xbin/mv", "/system/xbin/nanddump", "/system/xbin/nandwrite",
"/system/xbin/nbd-client", "/system/xbin/netstat", "/system/xbin/nice",
"/system/xbin/nohup", "/system/xbin/nslookup", "/system/xbin/ntpd",
"/system/xbin/od", "/system/xbin/patch", "/system/xbin/pgrep",
"/system/xbin/pidof", "/system/xbin/ping", "/system/xbin/pipe_progress",
"/system/xbin/pkill", "/system/xbin/pmap", "/system/xbin/poweroff",
"/system/xbin/printenv", "/system/xbin/printf", "/system/xbin/ps",
"/system/xbin/pstree", "/system/xbin/pwd", "/system/xbin/pwdx",
"/system/xbin/rdev", "/system/xbin/readlink", "/system/xbin/realpath",
"/system/xbin/renice", "/system/xbin/reset", "/system/xbin/resize",
"/system/xbin/rev", "/system/xbin/rm", "/system/xbin/rmdir",
"/system/xbin/rmmod", "/system/xbin/route", "/system/xbin/run-parts",
"/system/xbin/rx", "/system/xbin/sed", "/system/xbin/seq",
"/system/xbin/setconsole", "/system/xbin/setserial",
"/system/xbin/setsid", "/system/xbin/sh", "/system/xbin/sha1sum",
"/system/xbin/sha256sum", "/system/xbin/sha3sum",
"/system/xbin/sha512sum", "/system/xbin/sleep", "/system/xbin/sort",
"/system/xbin/split", "/system/xbin/stat", "/system/xbin/strings",
"/system/xbin/stty", "/system/xbin/sum", "/system/xbin/swapoff",
"/system/xbin/swapon", "/system/xbin/sync", "/system/xbin/sysctl",
"/system/xbin/tac", "/system/xbin/tail", "/system/xbin/tar",
"/system/xbin/taskset", "/system/xbin/tee", "/system/xbin/telnet",
"/system/xbin/telnetd", "/system/xbin/test", "/system/xbin/tftp",
"/system/xbin/tftpd", "/system/xbin/time", "/system/xbin/timeout",
"/system/xbin/top", "/system/xbin/touch", "/system/xbin/tr",
"/system/xbin/traceroute", "/system/xbin/true", "/system/xbin/ttysize",
"/system/xbin/tune2fs", "/system/xbin/umount", "/system/xbin/uname",
"/system/xbin/uncompress", "/system/xbin/unexpand", "/system/xbin/uniq",
"/system/xbin/unix2dos", "/system/xbin/unlzma", "/system/xbin/unlzop",
"/system/xbin/unxz", "/system/xbin/unzip", "/system/xbin/uptime",
"/system/xbin/usleep", "/system/xbin/uudecode", "/system/xbin/uuencode",
"/system/xbin/vi", "/system/xbin/watch", "/system/xbin/wc",
"/system/xbin/wget", "/system/xbin/which", "/system/xbin/whoami",
"/system/xbin/xargs", "/system/xbin/xz", "/system/xbin/xzcat",
"/system/xbin/yes",
"/system/xbin/zcat");
symlink("libGLESv2.so", "/system/lib/libGLESv3.so");
symlink("mksh", "/system/bin/sh");
symlink("toolbox", "/system/bin/cat", "/system/bin/chcon",
"/system/bin/chmod", "/system/bin/chown", "/system/bin/clear",
"/system/bin/cmp", "/system/bin/cp", "/system/bin/date",
"/system/bin/dd", "/system/bin/df", "/system/bin/dmesg",
"/system/bin/du", "/system/bin/getenforce", "/system/bin/getevent",
"/system/bin/getprop", "/system/bin/getsebool", "/system/bin/grep",
"/system/bin/hd", "/system/bin/id", "/system/bin/ifconfig",
"/system/bin/iftop", "/system/bin/insmod", "/system/bin/ioctl",
"/system/bin/ionice", "/system/bin/kill", "/system/bin/ln",
"/system/bin/load_policy", "/system/bin/log", "/system/bin/ls",
"/system/bin/lsmod", "/system/bin/lsof", "/system/bin/md5",
"/system/bin/mkdir", "/system/bin/mkswap", "/system/bin/mount",
"/system/bin/mv", "/system/bin/nandread", "/system/bin/netstat",
"/system/bin/newfs_msdos", "/system/bin/notify", "/system/bin/printenv",
"/system/bin/ps", "/system/bin/r", "/system/bin/readlink",
"/system/bin/renice", "/system/bin/restorecon", "/system/bin/rm",
"/system/bin/rmdir", "/system/bin/rmmod", "/system/bin/route",
"/system/bin/runcon", "/system/bin/schedtop", "/system/bin/sendevent",
"/system/bin/setconsole", "/system/bin/setenforce",
"/system/bin/setprop", "/system/bin/setsebool", "/system/bin/sleep",
"/system/bin/smd", "/system/bin/start", "/system/bin/stop",
"/system/bin/swapoff", "/system/bin/swapon", "/system/bin/sync",
"/system/bin/top", "/system/bin/touch", "/system/bin/umount",
"/system/bin/uptime", "/system/bin/vmstat", "/system/bin/watchprops",
"/system/bin/wipe");
symlink("/system/vendor/firmware/fw_bcm4329.bin", "/system/etc/firmware/fw_bcm4329.bin");
symlink("/system/vendor/firmware/fw_bcm4329_apsta.bin", "/system/etc/firmware/fw_bcm4329_apsta.bin");

while cat $ups | sed -e '/^set_perm/,/);/!d' gives you

set_perm(0, 0, 0777, "/tmp/installswap.sh");
run_program("/tmp/installswap.sh");
set_perm(0, 0, 0777, "/tmp/check_data_apps.sh");
run_program("/tmp/check_data_apps.sh");
set_perm_recursive(0, 0, 0755, 0644, "/system");
set_perm_recursive(0, 0, 0755, 0755, "/system/addon.d");
set_perm_recursive(0, 2000, 0755, 0755, "/system/bin");
set_perm(0, 3003, 02750, "/system/bin/netcfg");
set_perm(0, 0, 0755, "/system/bin/ping");
set_perm(0, 2000, 0750, "/system/bin/run-as");
set_perm(1014, 2000, 0550, "/system/etc/dhcpcd/dhcpcd-run-hooks");
set_perm_recursive(0, 2000, 0755, 0755, "/system/etc/init.d");
set_perm(0, 0, 0755, "/system/etc/init.d");
set_perm_recursive(0, 2000, 0755, 0644, "/system/vendor");
set_perm(0, 0, 0644, "/system/vendor/etc/audio_effects.conf");
set_perm_recursive(0, 0, 0755, 0644, "/system/vendor/firmware");
set_perm(0, 2000, 0755, "/system/vendor/firmware");
set_perm(0, 0, 0644, "/system/vendor/lib/libbt-vendor.so");
set_perm_recursive(0, 2000, 0755, 0755, "/system/xbin");
set_perm(0, 0, 06755, "/system/xbin/librank");
set_perm(0, 0, 06755, "/system/xbin/procmem");
set_perm(0, 0, 06755, "/system/xbin/procrank");
set_perm(0, 0, 06755, "/system/xbin/su");
symlink("/system/vendor/firmware/fw_bcm4329.bin", "/system/etc/firmware/fw_bcm4329.bin");
set_perm_recursive(0, 1001, 0755, 0775, "/system/etc/ppp");
set_perm(0, 0, 04755, "/system/bin/pppd");
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(1002, 1002, 0440, "/system/etc/dbus.conf");
set_perm(1014, 2000, 0550, "/system/etc/dhcpcd/dhcpcd-run-hooks");
set_perm_recursive(0, 2000, 0755, 0644, "/system/vendor");
set_perm(0, 2000, 0755, "/system/vendor/lib");
set_perm_recursive(1000, 1000, 0771, 0644, "/data/app");

the two run_programs shouldn't cause any real issues - it's more of a cosmetic issue.

Edit. The only thing I think that fits is that its searching in batches where each batch is seperated by a blankline, and within each batch it's searching for the pattern ( set_perm ) within each batch and displays the lines from the first occurance to the last, if that's the case then it working as well as it has is a bit of fluke then I'd take it.

Edit2. The above doesn't just quite fit to what's actually happening.