I'm pretty sure that there is an scene of Logan trying to kill Kurt in a training early in CC run, but i had been a while, so maybe i'm wrong. There is another time when Logan attacked Kurt again, that happened after The Dark Phoenix Saga, like you mentioned, but that was different, it was to showcase that Wolverine has problems controlling his more animal side (Logan attack him for kissing Mariko in the cheek right before a date) and he feel ashamed about it, it was i usually headcannon that Logan more innapropiate advances to Jean were partially happening because of that (as i said he has more problems controlling his feral nature after Weapon X). I don't remember the exact issue, but i'm pretty sure that is the same one where Kitty stayed alone in the mansion and fought a Broo.