Basically, the fence Koopas always show up in front of the fences. I don't know what's causing it? (See the bottom Koopa)

iirc this is a problem with the tileset slot that you are using, the koopa should go behind it only if the fence tile is in the exact same position in the original castle tileset with the fence
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Youtube - GitHub - NSMB Central

The problem is that the fence Koopas can only go behind 3d graphics. For the Tower/Castle tilesets the climbable fence tiles are replaced with quads that are drawn with the 3d engine.
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GitHub - Kuribo64 - YouTube

those graphics are in the polygon_unit folder like every other 3D tiles.
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Nothing to say, so jadnjkfmnjamnfjkldnajfnjkanfjdksan jsdnvj m.

I've been at it for around an hour now, the Koopas show correctly behind the fences but now the tileset is messing up, I replicated everything from the original Tower tilesets but as you can see, it's messed up. The Koopa at the top won't go up or down, and the bottom one (behind the fences!) just spins in place.

EDIT: Disregard this. I had forgotten the most crucial thing, Tile behavior. Oops.
EDIT2: After setting the tile behavior, they show up in front again. I'm extremely confused.
Also, is there a way to remove the conveyor belt animations?