Do you want to keep something from your old emunand on the old sd card? like installed games etc.
If not, then you can setup a fresh emunand on the new sd card. (like
@Garro suggested)
If you create a new emuNAND, this is a copy of your sysNAND.
So every clean up before the creation of the emuNAND is not necessary.
In Method 1:
Format sysNAND and delete "Nintendo 3DS" folder
You don't need to clean up these things.
Edit:
I forgot, that you used Gateway Emunand.
So I'm not sure, how the process of creating a emuNAND is there, but the things above should hold.