What is the cheapest lv40 item that I can buy from a NPC shop?

I'm not calling you a liar or anything as I see no reason why you would do such but that doesn't really make any sense. The crystal itself states it is obtained from items lv40 to lv60 items. If it does then it must be an oversight or you just got extremely lucky as the crystals do have a chance of upgrading and it could be possible that you got lucky and nothing became a basic item crystal.

I see no harm in trying though and I believe you can buy them from a guy in Henesys. So I'll give it a shot and give my results when I do it unless someone else beat me to it.

And Advanced Item Crystals state that they come from 100-130, yet level 95 items give them too.
Confirming that they still do, just tested it on my mule with multiple hats, got each time.