I love Touhou and have a very hard time arranging my favorite characters, eh-heh.

Anyway, um... it really is a matter of... Hmm. The only real "skeleton youkai" that I feel works in the setting is a Gashadokuro, which is... way too big and monstrous for this and is also the physical manifestation of the spirits of people who died from starvation as I recall. ^^;

The closest thing I can think of to this that works with the mechanics of the setting(I'm so sorry I don't have more written out on this matter) would be animating a skeleton using necromancy.