[AT&T Samsung Galaxy Note I717] darkspr1te:
Most boot loops occur on firmware changes either due to , incorrect firmware, not clearing cache, not resetting to factory , incorrect boot images or user error.

The su or root binary is just copied on to the /system/xbin folder , thats it , in some cases a copy of busybox is also placed there , here is a example from the updater script from the super user file i posted

ui_print("Applies only to E160");
ui_print("Created by qq10864333,All rights reserved");
ui_print("Sep-9th-2012 ");
ui_print("writing start!");

ui_print("Updating SYSTEM...");
mount("ext4", "EMMC", "/dev/block/mmcblk0p24", "/system");
delete("/system/app/Superuser.apk", "/system/bin/su", "/system/xbin/su", "/system/bin/busybox", "/system/xbin/busybox");
package_extract_dir("system", "/system");

symlink("busybox", "/system/xbin/[", "/system/xbin/[[",
"/system/xbin/arp", "/system/xbin/ash", "/system/xbin/awk",
"/system/xbin/basename", "/system/xbin/bbconfig", "/system/xbin/brctl",
"/system/xbin/bunzip2", "/system/xbin/bzcat", "/system/xbin/bzip2",
"/system/xbin/cal", "/system/xbin/cat", "/system/xbin/catv",
"/system/xbin/chgrp", "/system/xbin/chmod", "/system/xbin/chown",
"/system/xbin/chroot", "/system/xbin/cksum", "/system/xbin/clear",
"/system/xbin/cmp", "/system/xbin/cp", "/system/xbin/cpio",
"/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/expr",
"/system/xbin/false", "/system/xbin/fdisk", "/system/xbin/fgrep",
"/system/xbin/find", "/system/xbin/fold", "/system/xbin/free",
"/system/xbin/freeramdisk", "/system/xbin/fuser", "/system/xbin/getopt",
"/system/xbin/grep", "/system/xbin/gunzip", "/system/xbin/gzip",
"/system/xbin/head", "/system/xbin/hexdump", "/system/xbin/id",
"/system/xbin/ifconfig", "/system/xbin/insmod", "/system/xbin/install",
"/system/xbin/ip", "/system/xbin/kill", "/system/xbin/killall",
"/system/xbin/killall5", "/system/xbin/length", "/system/xbin/less",
"/system/xbin/ln", "/system/xbin/losetup", "/system/xbin/ls",
"/system/xbin/lsmod", "/system/xbin/lspci", "/system/xbin/lsusb",
"/system/xbin/lzop", "/system/xbin/lzopcat", "/system/xbin/md5sum",
"/system/xbin/mkdir", "/system/xbin/mke2fs", "/system/xbin/mkfifo",
"/system/xbin/mkfs.ext2", "/system/xbin/mknod", "/system/xbin/mkswap",
"/system/xbin/mktemp", "/system/xbin/modprobe", "/system/xbin/more",
"/system/xbin/mount", "/system/xbin/mountpoint", "/system/xbin/mv",
"/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/pkill", "/system/xbin/printenv",
"/system/xbin/printf", "/system/xbin/ps", "/system/xbin/pwd",
"/system/xbin/rdev", "/system/xbin/readlink", "/system/xbin/realpath",
"/system/xbin/renice", "/system/xbin/reset", "/system/xbin/rm",
"/system/xbin/rmdir", "/system/xbin/rmmod", "/system/xbin/route",
"/system/xbin/run-parts", "/system/xbin/sed", "/system/xbin/seq",
"/system/xbin/setsid", "/system/xbin/sh", "/system/xbin/sha1sum",
"/system/xbin/sha256sum", "/system/xbin/sha512sum",
"/system/xbin/sleep", "/system/xbin/sort", "/system/xbin/split",
"/system/xbin/stat", "/system/xbin/strings", "/system/xbin/stty",
"/system/xbin/swapoff", "/system/xbin/swapon", "/system/xbin/sync",
"/system/xbin/sysctl", "/system/xbin/tac", "/system/xbin/tail",
"/system/xbin/tar", "/system/xbin/tee", "/system/xbin/telnet",
"/system/xbin/test", "/system/xbin/tftp", "/system/xbin/time",
"/system/xbin/top", "/system/xbin/touch", "/system/xbin/tr",
"/system/xbin/traceroute", "/system/xbin/true", "/system/xbin/tty",
"/system/xbin/tune2fs", "/system/xbin/umount", "/system/xbin/uname",
"/system/xbin/uniq", "/system/xbin/unix2dos", "/system/xbin/unlzop",
"/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/yes",
"/system/xbin/zcat");

symlink("toolbox", "/system/bin/cat", "/system/bin/chmod",
"/system/bin/chown", "/system/bin/cmp", "/system/bin/date",
"/system/bin/dd", "/system/bin/df", "/system/bin/dmesg",
"/system/bin/getevent", "/system/bin/getprop", "/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/log",
"/system/bin/ls", "/system/bin/lsmod", "/system/bin/lsof",
"/system/bin/mkdir", "/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/reboot",
"/system/bin/renice", "/system/bin/rm", "/system/bin/rmdir",
"/system/bin/rmmod", "/system/bin/route", "/system/bin/schedtop",
"/system/bin/sendevent", "/system/bin/setconsole",
"/system/bin/setprop", "/system/bin/sleep", "/system/bin/smd",
"/system/bin/start", "/system/bin/stop", "/system/bin/sync",
"/system/bin/top", "/system/bin/touch", "/system/bin/umount",
"/system/bin/uptime", "/system/bin/vmstat", "/system/bin/watchprops",
"/system/bin/wipe");

set_perm(0, 0, 06755, "/system/bin/su");
set_perm_recursive(0, 2000, 0755, 0755, "/system/xbin");

unmount("/emmc");
unmount("/cache");
unmount("/system");
unmount("/data");
ui_print("ROOTED");

here is laymen version of whats happening, first it mounts the /system folder, then removes old busybox/su binary then extract the two files in the update.zip in /system folder , one in /system/bin one in /system/xbin

then is creates a bunch of symlinks to busybox binary file (the program detects what filename it's run as and pretends to be that program)

my zip also includes the two tools to manage which programs can execute su binary.

it's worth noting that older busybox version did not have all the tools required built in yet a symlink was created for it, this would break parts of the system as a program would try and access say chmod and busybox does not know what to do, that would create boot loops if the booting system relied on functions busybox replaced. again, its user error.

to avoid this, use the backup functions of twrp/cwm recoveries before you apply the root.

darkspr1te