The skin xml can make a ton of template changes (and clearly did). Mixing skins with mods is hard - and the same is true on any board. I personally don't use skins that have template changes on my boards because they are so heavily moded, and even if I made all the changes needed to get the mods to work, it's an upgrade nightmare.
Again, I'd suggest having one of the many very good designers here at the org make you a custom skin with min. template edits.
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