[Verizon Galaxy Note 3 Q&A, Help & Troubleshooting] bftb0:
out of curiosity I did a differential comparison of the system.img between the stock and "rooted" versions that [MENTION=4708661]muniz_ri[/MENTION] provided.

e.g.

$ echo 'Samsung NK1 stock system'
$ [b]simg2img[/b] stock_system.img.ext4 raw_system.img.ext4
$ su /bin/bash
# mkdir /tmp/nk1
# losetup /dev/loop0 raw_system.img.ext4
# mount -t ext4 -o ro /dev/loop0 /tmp/nk1
# (cd /tmp/nk1 ; find . -type f -exec md5sum {} \; ) 2>&1 | tee stock_system_md5s.txt
# chown user.user stock_system_md5s.txt
# umount /tmp/nk1
# losetup -d /dev/loop0
# rm raw_system.img.ext4

# echo 'Rooted NK1 system - not in sparse format, no need for simg2img'
# losetup /dev/loop0 rooted_system.img.ext4
# mount -t ext4 -o ro /dev/loop0 /tmp/nk1
# (cd /tmp/nk1 ; find . -type f -exec md5sum {} \; ) 2>&1 | tee rooted_system_md5s.txt
# chown user.user stock_system_md5s.txt
# umount /tmp/nk1
# rmdir /tmp/nk1
# losetup -d /dev/loop0
# exit
$
$ echo 'here is the magic'
$ cat rooted_system_md5s.txt stock_system_md5s.txt | sort +1 -2 | uniq -u 2>&1 | tee unique_file_listing.txt

The listing produced is all unique files between the two system images; note they can be unique for two reasons:

(1) A file of that path-name is only present in one but not the other (a file is deleted from one or added to one)

(2) A file of that path-name is present in both but has been modified. You'll see duplicate file path-names in this case.

Having done this comparison for the system images, some things seem rather evident in [MENTION=4708661]muniz_ri[/MENTION] deltas; but others are less obvious (note lib/libsupol.so appears in the rooted version)

e75410f8e31fe505adb26d6a07725689 ./app/Superuser.apk
04cdb55b01d687afa2e085e300cdbe77 ./bin/ddexe
c8bc38e34a3d0456de08f06ec6102956 ./bin/ddexe
c8bc38e34a3d0456de08f06ec6102956 ./bin/ddexe_real
c2d5c3f94c41024eedb4569779597cf6 ./bin/.ext/.su
7beeb0980b778711a4ca30c78a418346 ./csc/contents.db
d514e14350f60f8d6a72aabd6d505722 ./csc/customer.xml
9279436a75cb1012f9999aec603beb33 ./csc/default_application_order.xml
a78afd02d69756736fd8df51776fe588 ./csc/default_workspace_cp.xml
2d46ed4aacf78532d176fbcc0ccdde8f ./csc/default_workspace.xml
b72d13ff1e0e383fa513768313a85c58 ./csc/easylauncher_default_workspace.xml
7f8bb831c5ebbe1d9ad2148dfd57a5b4 ./csc/feature.xml
ab29f88da583a4e04c4d5be423b9ca06 ./csc/others.xml
e17ce2e847276854abf3ec37ca592d4a ./csc/sales_code.dat
2a2931bfef9a2d7c8fd5b6f93e3917c9 ./CSCVersion.txt
fc48464a541cf5dc039f1147f7365e1a ./etc/autorun.iso
d41d8cd98f00b204e9800998ecf8427e ./etc/csc_apks_list.txt
d41d8cd98f00b204e9800998ecf8427e ./etc/csc_remove_apks_list.txt
d41d8cd98f00b204e9800998ecf8427e ./etc/csc_ringtones_list.txt
d41d8cd98f00b204e9800998ecf8427e ./etc/csc_user_apks_list.txt
d41d8cd98f00b204e9800998ecf8427e ./etc/csc_user_remove_apks_list.txt
45f27ea81dacdd6ba8a0722bd1065d01 ./etc/enforceskippingpackages.txt
d41d8cd98f00b204e9800998ecf8427e ./etc/hidden_apks_list.txt
b026324c6904b2a9cb4b88d6d61c81d1 ./etc/.installed_su_daemon
75fe72f2c977635bf2182a1be274345b ./etc/install-recovery.sh
acb73ff1de53675b420a7b14b9eac263 ./finder_cp/cpdata.xml
98357ec8dd72bbcdc39677204bfe05a4 ./finder_cp/web_cp_logo_baidu.png
abea7fc2866484fe9bb86e5aa9b98d6d ./finder_cp/web_cp_logo_bing.png
529173df0ef025a403fa5e0af5bc05df ./finder_cp/web_cp_logo_daum.png
8809f9b7fcdb679a0d66c8c7e7271281 ./finder_cp/web_cp_logo_google.png
58400ecde3dc101babed2a5db8c5a95d ./finder_cp/web_cp_logo_naver.png
c9b13d0610cd161ef48ac69796627d8f ./finder_cp/web_cp_logo_yahoo.png
c2ca061f4f83b44dc6a01579c8236493 ./hidden/INTERNAL_SDCARD/mobitv/dca.config
d84e60fbfe2f9aea6c2fbf268fb9fa8a ./hidden/INTERNAL_SDCARD/mobitv/foa.config
863ed2e929f24ad577905e92308a8800 ./hidden/INTERNAL_SDCARD/Samsung/Music/Over_the_horizon_2013.mp3
8d97de61b73bc6345001aab0e5b2cfdf ./lib/libsupol.so
b00734ca4cbc75ab17e7f04d7d72606f ./sipdb/en_US.zip
e7d85e3154308a40cba592273b34fcc0 ./sipdb/es_US.zip
56e0a71b160da01cbacdd606f6a21d0c ./sipdb/ko_KR.zip
86661c0d2d76cebf4f2f98e5cedb1fba ./sipdb/vi_VN.zip
5b43113a786dd197457a7da544e417bf ./sipdb/zh_CN.zip
bedf281b2ca0cea7b578c56146f61cfb ./SW_Configuration.xml
d41d8cd98f00b204e9800998ecf8427e ./VODB/en_US/checked
3fab613e69ed7bbdb4037227f40b3e93 ./VODB/en_US/en_US-ak-cur.lite.res
d2c7826b54f158388d5d631f7cc4eb94 ./VODB/en_US/en_US.lang
fbb63aed41785d843a3ede94dd5ebba5 ./VODB/en_US/en_US-lk-text.lite.res
d0fddf901a952652d327db6d353c39c5 ./VODB/en_US/files.txt
d41d8cd98f00b204e9800998ecf8427e ./VODB/es_US/checked
37233ae458dc58cce4e1cf3dfc7199bf ./VODB/es_US/es_MX-ak-cur.lite.res
de0e1db152031b405c3f94786519553b ./VODB/es_US/es_MX-lk-text.lite.res
95bf163ae41a21bfb03bde5994d32b47 ./VODB/es_US/es_US.lang
1f5d5bb76aacf2ecaf4efaede1d2de27 ./VODB/es_US/files.txt
d41d8cd98f00b204e9800998ecf8427e ./VODB/ko_KR/checked
f147743aa0e4c81acb66bde88e540cb7 ./VODB/ko_KR/files.txt
daf9861d29a51e989c9a4349cab1f0d2 ./VODB/ko_KR/ko_KR_johab-ak-cur.lite.res
d8598fec91290155e692b48e35c00c14 ./VODB/ko_KR/ko_KR_johab-lk-text.lite.res
ce79e020530910f70cf99e1ef075338d ./VODB/ko_KR/ko_KR.lang
d41d8cd98f00b204e9800998ecf8427e ./VODB/vi_VN/checked
1826e916c633326238aece3f625068d8 ./VODB/vi_VN/files.txt
93dd91b00a3aa970f6cd287a51c86eb8 ./VODB/vi_VN/vi_VN-ak-cur.lite.res
a7858ae999d0595bed5364d116df7f90 ./VODB/vi_VN/vi_VN.lang
ee7501f7588d98febaafa095a8bab689 ./VODB/vi_VN/vi_VN-lk-text.lite.res
d41d8cd98f00b204e9800998ecf8427e ./VODB/zh_CN/checked
8507d9d93801d26c0c112f913aa4a1c0 ./VODB/zh_CN/files.txt
c914ab0bf6f02ea6c607813d4a60d911 ./VODB/zh_CN/zh_CN_gb18030-ak-cur.lite.res
a992e77a706e8be8b182d2829b946069 ./VODB/zh_CN/zh_CN_gb18030-lk-text.lite.res
1d1b38601002c263be46a7970f427aba ./VODB/zh_CN/zh_CN.lang
c6d2482325d35384ce19e34723bb7652 ./wallpaper/lockscreen_default_wallpaper.png
c2d5c3f94c41024eedb4569779597cf6 ./xbin/daemonsu
c2d5c3f94c41024eedb4569779597cf6 ./xbin/su
c2d5c3f94c41024eedb4569779597cf6 ./xbin/sugote
57dd3b21dfb238a3065299851db9fc91 ./xbin/sugote-mksh
521005a1a9a03e118db633e9626b7221 ./xbin/supolicy

Obviously, you will want to unpack the boot images & their ramdisks and follow a similar forensic procedure there.

Hope this helps. Obviously, this is not a comprehensive - for instance it won't flag differences in meta-data such as file modes (permissions), ownership, or extended attributes (which is how SElinux characteristics are stored). Those could easily also create issues if they differ.