Patch 2.0 reorganized the MPQs, removing a lot of repeated Data. the result is a 4 gig wow folder instead of 6+. Everything from Model, texture, wmo, etc are in Common. New patch data is in Patch.mpq, the locale-enUS folders and MPQs hold DBC and interface files.
Second, get the newest MWCS from the Model Editing programs thread. Any other versions will crash upon clicking an M2 to the changed structure of the file.
Thirdly, you need to run the ModelChangeFix every time you run a swap other than a creature weapon swap. Also textures are fine. Anything else, including Character, any world m2 swap, WMO, ADT and DBC require it. It is a hack.
That's about all. Every swap from before works, except Spell.dbc. Stay away from that. And welcome back.