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_filesDo 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!