I couldn't yet give that tutorial a thorough read, and it's been quite a while since I last worked with custom heads, but I created my dragon's head mesh from reshaping the Vanilla Argonian head myself those years ago, following all guides and warnings current back then.
I also didn't feel like recreating from scratch 100+ custom morphed copies of my head in order to be able to create "new" EGM (shape morphs) and TRI (facial animation morphs) files from them. So it was paramount for me to never touch the vertex count and/or order in the process, a lot like what you seem to have done here.
I did have to run the EGM and/or TRI file (can't remember which one anymore) through Scanti's Conformulator once though, as there were still some oddities when using the Vanilla ones directly with my new head. But I'm not seeing any of what I ran into (e.g. exploding teeth when opening mouth) in your case here either.
It does look, however, kinda like your head mesh isn't "rigged" to the neck and head armature anymore from the huge gap in its throat. Pictures don't give it away, but does it "bend" when turning left and right or looking up and down?
I remember my first export didn't have rigging info attached (possibly a weakness of the file type I was told to use) and I had to re-rig the resulting head NIF myself first.
But heads are a rather troublesome business in Oblivion modding anyways.
Quite often they're lying sideways in their NIF and are positioned at the 0 point. Only rarely did I see any with a complete armature and at their correct place above the neck rotated upright.
And did you ever notice the "unapplied" transformation (translations moving them from the 0 point up to the neck connector) these heads have in their NIFs? Those are so inside the NiTriShape/Strips node the internal vertex locations are still around the 0 point, so all morphs (0-based offsets per vertex each) still work, yet it "appears" to be sitting on your neck.
If you changed anything about the border line around the neck of your head, these unapplied offsets might also have to be adapted accordingly until it fits.
But this is so above my pay grade and I'm only telling from very faint memories of my own attempts, fails and final success here now. So take all I said with a grain of salt and read up more expert guides or knowledge about it than what I got.
I was totally unable to re-do what I did the first time around with my current up-to-date new dragon head mesh also multiple times I tried, so... What could I possibly have learned, if I can't "reproduce" the previously successful result?