I just wanted to say thank you again to @AndikaTedja
for this extremely useful tool!
For anyone interested, this worked perfectly on my Samsung Galaxy Tab 4 10.1 SM-T530NU on build no. UEU1ANK1 4.4.2 KitKat. Main.bat wasn't able to pull the required directories, so I did that myself using ES smb. Other than that everything worked exactly as it should, I chose the option to zipalign too. I was able to flash the zip file created by the tool in TWRP 188.8.131.52. Just remember the first boot will probably take a very long time, so be patient and make sure your battery is charged before trying this.