I personally do not do it by hand, I have made my own script and batch file to do this for me.
But it's so simple, you'll be wondering why no one has figured it out yet, or if they have, no one has said anything about it yet.
EDIT(February 4th, 2015): Remade the tutorial, this is for Terker for asking for it.
Youtube Link: https://www.youtube.com/watch?v=6mpzcXU3qJU
It's so simple you'll wonder why no one has figured it out yet.
Tools You'll need:
♠♠010 Editor: http://www.sweetscape.com/
♠♠010 Editor Templates: http://modcraft.superparanoid.de/vie...php?f=59&t=828
---Account needed to download templates, Scroll down to Dahaga's Post for the Download.
♠♠WMO Wiki: http://www.pxr.dk/wowdev/wiki/index....v17#MODD_chunk
♠♠CASC Explorer: https://github.com/WoW-Tools/CASCExplorer/releases
Thanks goes to: The guys over at pxr.dk , My Subscribers/Followers, Indirect Inspiration and motivation from steff, soldan, vlad, will, fearless_wind, Gamh, Mjollna, BanzBoyz77, ToxicDev, Vynlendus, and more, too many to list!
EDIT/UPDATE(March 15th, 2015)
Made a Video covering a slightly harder to convert WMO which will require a bit more work than just simply deleting a chunk.:
Click The Image for the Video or Click Here: https://www.youtube.com/watch?v=9tI26ShuEgc
Images of my converted wmos:
---It's Red because I pulled it from 5.4.0, 5.2.0 and back has yellow lights.
---Scrolls on fire because of 5.4.0 pull I think.