ah. so you have effectively made a new head. < adding or removing vertices to it at this stage is completely irrelevant. you have changed the vertex order now. so the list is different. this will invalidate the the vanilla khajiit tri/egm files.
well you could *try to use the conformulator. just export as a nif as usual. so its rigged and set up for game etc. then export it as an obj from nifskope. then use that to and the vanilla tri to get the new tri and egm.
If you moved vertices around the mouth and eyes. then the conformulator will not be able pass the morphs onto this new topology very well. so the face expressions may likely be a bit weird.
They only other way to do it is make all the morphs by hand in max. then see if you can export them properly... then use addmorph to pack them into a tri file. < this is no easy feat. but can be done. I have possible solutions to getting it to work. I'm not modding oblivion anymore so I can't really test any of my experiments. last time i tried though, the exporter was reordering the vertex list, between base head and morphs... fubar.
or use facegen customizer to make custom tri files.
If i look at the nif files of the vanilla Khajiit Head it has some Vector Settings like "X 0.0000" - "Y -1.1870" - "Z 112.4410" so if i set all these to 0 the head is on the "ground" but i can't apply that to my head.
I didn't a complete new mesh, i just moved the verticles a bit.
that XYZ positioning is probably the meshes pivot center. that is actually the position of the bip01 head bone when you import it into the max scene.
why mess with them :S
you did make a new mesh, or at least you tricked everything into thinking you did/ you imported it and exported it. this is enough to reorder vertices. never mind if you ever collapsed a modifer stack or anything like that. < which deffinitely reorders vertex lists
one method would have been to import the vanilla head. add the edit poly collapse, chnage UVs etc. now clone it.
only work on the clone and DO NOT reoder vertices. now skin them both.
export both to a nif.
HOPEFULLY you have 2 identical meshes, one you are going to use to convert the morphs to. the other is the one you will use in game. save max scene < check vertex order by using a morpher modifier, if it works, just reload the max scene before you added the morpher. just being really careful

export both heads into 1 nif
so export the one that is unedited as a obj from nifskope. make tri from the vanilla head.
delete that head you don't want from the nif.
now set up the head, tri/egm/egt etc and test
the morphs around the mouth will likely not be passed over correctly. what you have to do is slightly open the mouth a bit, the conformulator can't tell which vert opens up or down when the mouth moves, as the verts on the top and bottom of the mouth are sharing the same object space