What do you think of this? It doesn't have the extra little cutouts that your Z has, but it has to be better than just blanking out the model completely. Here's a link to an IPS patch. It shouldn't change anything except the X model, so you should be able to apply it directly to your hack if you want.
I was kind of intrigued when I saw DarkSamus's post breaking down the model data and tried my hand at making a model editor (which is what I used to make that Z model).
It looks nicer than it actually is, I think. It's not super user-friendly (clicking in the viewports does nothing, you have to use the controls on the right to edit everything), and it probably has some bugs (the perspective rotation doesn't behave quite like you'd expect because I don't know jack about 3D math), but it does work.
Right now the only model it can edit is the title screen X. I have no idea where any of the other model data is in the ROM. If DarkSamus (or anybody) knows the location for any of the other model data I might be able to make them all editable. For this hack in particular it might be nice to change the X head model from the intro.
Here's a link to the editor if anyone wants to mess around with it. It comes with the Z model, and a model of a cube.
EDIT: The IPS patch I linked originally didn't work. I should have tested it before uploading. I've edited that link to one that should work.
Sorry for my late response but Wow, that looks great. I applied the patch to the hack and it looks good too.