The SCP that I am writing changes the internal organs of the subject it is used upon. I originally thought of referring to the subject as SCP-XXXX-2, but I've seen several SCP pages that just refer to them as "Subjects." The only thing is, these changes are really what make the SCP unique. Should those affected be referred to as SCPs, or subjects?
That is a good question and I myself would like to know that answer.
Grammar and spelling fixed by Bright.
If the changes are what comprise the main body of the SCP, and you're planning on referring to a number of subjects afflicted by it, refer to them as XXXX-2, -3, etc. If the subjects' organs are changed, and that's that, they can stay as subjects. A subject is only numbered if they become an instrument of the SCP's will or act in a capacity that would necessitate needing to designate them as another part of the SCP's effect. If they are more than just a victim, then the subject becomes as part of the effect as the actual SCP. But I would need a draft to give you a sure answer.
The SCP transmutes all internal organs into a single mass of metal that effectively renders the subject invincible, and I was thinking of refering to the person as SCP-XXXX-2 and the metal itself as SCP-XXXX-3. There are some strings attached to this protection, but the effects are what characterize the SCP.
I'm assuming you will go into detail about the composition of the metal so yes, numbering it will be okay. I suggest you refer to subject himself as only XXXX-2, since different designations for the person and the metal the person is comprised of is unnecessary.