So Bovi's checker wasn't particularly useful for figuring out what was wrong, all it told me was that no units used those animation sets, which I already knew. Luckily your devkit appears to have helped me a bit more to figure out where the error was caused, if not much else.
The error occurs when it comes to the Flamethrower animations:
Code:
12:35:16.777 [system.io] [info] exists: missing mods/devkit/data/siege_engines/UnitModelsRefPoints/Flamethrower_Ref_Point.modelReferencePoints12:35:16.777 [system.io] [trace] file open,,data/siege_engines/UnitModelsRefPoints/Flamethrower_Ref_Point.modelReferencePoints,163
12:35:16.777 [system.io] [info] open: found data/siege_engines/UnitModelsRefPoints/Flamethrower_Ref_Point.modelReferencePoints (from: C:\Program Files (x86)\Steam\steamapps\common\Medieval II Total War)
12:35:16.777 [system.io] [info] exists: found mods/devkit/data/animations/MTW2_Musket/MTW2_Musket_basepose.cas (from: C:\Program Files (x86)\Steam\steamapps\common\Medieval II Total War)
12:35:16.778 [system.io] [info] exists: found mods/devkit/data/animations/MTW2_Flamethrower/MTW2_Flamethrower_knockback_from_front.cas (from: C:\Program Files (x86)\Steam\steamapps\common\Medieval II Total War)
12:35:16.778 [system.io] [trace] file open,,mods/devkit/data/animations/MTW2_Flamethrower/MTW2_Flamethrower_knockback_from_front.cas,8945
12:35:16.778 [system.io] [info] open: found mods/devkit/data/animations/MTW2_Flamethrower/MTW2_Flamethrower_knockback_from_front.cas (from: C:\Program Files (x86)\Steam\steamapps\common\Medieval II Total War)
12:35:16.809 [system.rpt] [error] Medieval 2: Total War encountered an unspecified error and will now exit.
All of these animations existed even before I tried to put these animations in the descr_skeleton file. I'm not even sure what I could do differently, because the entries for these animations are pulled directly from the kingdoms descr_skeleton file.