Hi everyone! Well, I did it. I slaved over this issue for weeks and finally figured out how to solve it. This glitch occurs when a member of your party vanishes during battle while riding Magitek Armor. The game accidentally draws both the disappearing and reappearing animations over the armor, so the legs become visible outside the armor. This patch ensures that the characters' legs never become visible while they are riding Magitek Armor.
And while I'm at it, there's another issue that's been stressing me out just as much: Doom only taking away a character's upper body when they are riding Magitek Armor. There's documentation on Slick Productions that includes the C1 bank, so you can see the code at C1/3D43 surrounding the JSR I added to replace a CMP. Basically, the Vanish animation manipulates the sprite data stored in RAM at 7F:0000-7F:A000, so to fix this glitch I made sure the legs wouldn't be stored there for characters riding Magitek Armor. When a character reappears, the sprite data there is repopulated with the sprite data in the ROM at D5/0000 onwards. I'm thinking I need to do something similar with the Doom animation. I need to find the area of the code where it grabs data for the sprite that gets hauled off by the reaper and force it to include the legs.

December 13, 2015
Fixed a problem with the patch whereby it sometimes wasn't including the legs at all, because the code that checks if a character has Magitek status was grabbing data from the wrong place in RAM. This problem is now fixed. I recommend re-downloading this patch.

February 11, 2016
Fixed a patch-breaking problem; the patch was adding the free space in the wrong place. The free space overlapped with the last three bytes of the Magitek-check function, breaking it. As I said, this problem has now been fixed.

February 11, 2016
Fixed another patch-breaking problem with the 1.0 patch; I'd failed to make the necessary adjustments to some of the JSRs. Also made a correction to the Magitek Armor check function; it was still loading from the wrong place in RAM and I'd somehow failed to notice.

March 21, 2016
Discovered a RAM byte that allows for some added efficiency. Re-downloading is optional, but recommended.