When adding a custom spell ID in aurawatch on classic it does not show up.

When doing it with LUA it does show up.

From GUI settings you can only add to Custom CD.

How did you do in LUA? Can you post it here?

Just go directly to file (per class) and add the spell there Interface\AddOns\NDui\Config\AuraWatchList and add my spells there as from GUI it is not working

I meant what did you write in lua file, post it here then I can tell what's wrong in it

From lua i do not have issues I can add my spells.

The issue is only for UI ingame (add any spell and it will not work)

Just do as I told!
Once you post your edit in here, I can tell why you cant add in ui. And tell me how you did in game ui might be helpful as well.
There shouldn't be any issue in the ui itself.
So what is the difficulty among the conversation for talking such a long period?