First you must be rooted with custom recovery. either CWM or TWRP will do.
1. Download THIS FILE Credit to anbech
(THIS FILE disables the above action.)
2. Flash the above file, reboot. done
3. Add the zip file of the animation you want to //system/media with the permissions RW-R--R-- Make sure to rename the zip file bootanimation.zip after you download it
This should let your phone use the bootanimation.zip files that stock android ROMs use (Tested on GM900f 4.4.2)
NOTE, this only covers the booting up animation. the ROM will will still use shutdown.qmg to do a shutting down bootanimation.
Again all credit for this goes to anbech the following posts ill be adding my collection of ZIPS.