So I've updated to 2.3b and also I've got EmuNAND working for the first time. Aside from not updating before entering Gateway mode, is there anything else I have to look out for which could do damage to my system?
No, just make sure you see the GW3D before doing it, It's also advisable once you have updated your emunand to go back into sysnand and delete any internet settings it has remembered (they will be retained on emunand) so it will be pretty hard for you to accidentally update your sysnand.