So apparently in V0.9+ a bunch of core scripts related to equip were moved from RGSS to JSON, I'm guessing it messed most armor mods; the portraits from scenes look fine, it's just while walking the gear mismatches completely with Lona. I tried messing around with the GTC set mod for a while but no success so far, I hate to manually change RPG games due to how messy it is.
Remembered the recent problems with RolePlay-S mod which stopped working on the new version and the only option is to remake everything yourself manually. On the one hand the mod is broken on the other hand i wanted to test how broken it is but on the new version of LonaRPG it does't work. The picture problem is pretty simple shit though you can fix it quickly (sometimes) - and if I'm not mistaken the whole your problem was only here \LonaRPG\Data\CHSConfig - where you can just change layers of the AnyArmor.png like layers in photoshop.
Actually managed to fix the position of the armor... the actual .png image apparently mismatched Lona's body when overlapped so once I realized this it was pretty easy to fix with photoshop. Managed to fix the layering problem of the armor by adding it inside CHSConfig on the game files... tried to create a CHSConfig file inside the mod to avoid modifying game files but failed pathetically at trying the game to read it... I tried using this script but not sure if it even works...
module DataManager
self.singleton_class.send(:alias_method, :load_mod_database_YourModName, :load_mod_database)
def self.load_mod_database
tmpLonaCHS = FileGetter.load_lona_chs_settings_from_dir(folder="XXX",chsh=false)
The only thing I realized is that when you add or change something in LonaRPG files it's better not to pile on something new at all but to change the main thing and add a few script lines to the main file because when you try to create a new script the system still needs to explain specify separately how and what should work for it too, so that it can finally read it. In short... you're more likely to spend more time when you could just change or add a couple lines in the main CHS file. For such cases I always have a zip file LonaRPG to be able to return any file at any time if I do something wrong.