Converting each illustration to a vector format was required in order for the coloured pixels to change according to a user's chosen theme. Vector formats can also be a lot smaller in file size if properly optimized.
To prevent seams from appearing between the vectored pixels, I would extend shapes on lower layers so that shapes on higher layers would overlap. This could be a somewhat mind-numbing process, so I had to work hard to stay focused!
Here's what each layer looked like as they stacked higher, finally reaching the clean finished vector:
@Hapu 
actually created a tool that helped me test and make sure the finished vectors worked properly with user-chosen themes. Thanks again, buddy!
For a very quick look (SEIZURE WARNING, and loud music!) at the entire process, see the video here.
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