RTF is a global modification that replaces all towns in the game.

You can remove the arms and legs; I don't know much about skeletons. I would remove the hip bone and everything below it, but the Global bone needs to be kept, as it's the main one.

The Thunderlord can be fixed by giving it the animations from the Colossus and Titan.

I removed the Titan armor from the Inferno heroes in Heroes VI.