Well, some actual good news! I think I found the missing piece for sprites that I was missing so now I can set up new sprites!
The issue? Well, I have no clue what exactly the data MEANS.
This is the data that's read at 5D793 for Zero's open eye idle pose: 1A 00 80 31
This is the data that's read at 5D94F for Zero's first buster fir pose: 18 20 D9 31
Wait..I think I just figured it out for the most part. The "00 80" and "20 D9" is the area that it loads the graphics from ROM. I jumped to 188000 in Tile Molester and it's Zero's pose. Jumped to 18D920 and it's Zero's firing pose. I'm not sure what the 1A is yet and I believe "31" is the bank. I think I'll take a whack at this sometime but I think I'm going to take a break for now and recollect my thoughts.
Edit: Just took a test run. This basically is it, but some sprites went missing..strangely. Figured it out though! There's more than one chunk of data that loads per sprite to load the area it does!
Edit 2: The first custom sprite inserted into Mega Man X3! This is one of the frames that Zero will do when he's releasing Gravity Well/Ray Splash up into the air.