My bad. I confused the whole ordeal about armor parts. I confused "armor parts already being separated" with "X's overlapped sprites being complete sprites". I thought that maybe you could erase/override with blank space certain sections of the armor, but I see that is a far more complicated matter. Sorry for the misunderstanding.
However, I do have a possible alternative; instead of displaying the armor right away, display a different palette for X until he gets the complete armor (kind of like in X4 in which X had a special purple palette before he got the Ultimate Armor). Like maybe X's palette would be a much darker tone when using the Shadow Armor, or have it be a more neon green when using Blade Armor. I feel like it would be the best way of displaying an incomplete Armor, without displaying the complete armor, but being able to easily distinguish it from vanilla X. Again, these are just my ideas, and it's really up to acediez if he really wants to add it or not. Sorry if I sound very needy, I just really like contributing to this thread.