Then you must not be doing something right, I've used the procedure several times now.
You'll need to post a bunch more details for any of us to have a prayer of helping you with this.
Miax
What details do you need?
I opened up my earlier mesh (The one with the invisible parts) and the vanilla nif. I duplicate the base and replace the duplicates with parts from my earlier nif. I decide to remove one part of the weapon. I right click on that part, select body, and then Remove. I click Save As. I open up GECK and edit the Sawn Off Shotgun. I try to change the model. As soon as I change the model to my new model, it hangs for a few minutes and then crashes.