Resizing YrotN will result in floating characters if you don't take action. That's why size mods are quite time-taking. You need to make every animation stay the characters on the ground. As for the head, I think there's a bone that affects the turning. renaming it won't make changes if done the right way, but again you need to resize the bone in every animation.
You are sure it's those textures? Try removing them, redownload and if that won't work, try extracting the texture and insert them in a non-edited version.
I'm pretty sure it will be fixed with cleaning disc. I can happen at any time, so it must've been coincidence with Metroid. It happened to me before and it helped.
If you want to replace the stage, you'll need .rel files. If you want to replace it by a stage based on Final Destination, you'll need the .rel from Final Destination (st_final.rel) altered to have information from lylat cruise in it.
Go here: http://ssbbcustom.wikia.com/wiki/Module_files Do exactly as it says. In your case you'll need a st.final.rel with 13 instead of 2. Name the stage stgstarfox.pac and the .rel st_starfox.rel and there you go!