WDF:
As for extracting them, CptSky and Korvacs released a tool to extract them. If I am correct CptSky also released a tool to compress, not sure tho.
As for the shop, it depends on the patch. TQ started using emoneyshop starting from patch 5300?
The shop has a simple structure really,
its basically a header, npc id, npc name, npc type, purchase type (money or cps) and a list with items starting from 0 (just like an array).
All the maps have the puzzle files, they are just inside data.wdf.
C3 is a custom extension of TQ, they have even released the source of it. Spirited also shared the link including some explanation in one of his threads. So simply viewing them with OpenGL will most likely not work without adding the extension.