In respect to the set up question, you may just have to be a little more patient with that lifter. The lifter may also be thinking TOO much and just not allowing him/herself to get into the position that he/she feels like he/she knows. There could also be some muscular weakness. You said you tried GHDs, but maybe try some "swimmer" or "superman" drills to allow the lifter to feel the flex in the entire back. You can even do some presses/push presses behind the neck, along with some snatch presses from the squat. Additionally, some bent-over rows may help strengthen that area as well to help the lifter recruit those muscles in a more effective manner.
In regards to the valgus issue, I really wouldn't worry about it if it's happening with heavy weights, but if it's occurring with lighter weights, then the lifter can work on pause squats or simply keeping the knees in line with the toes and keeping the hips under the bar for the majority of the lift with lighter weights. I find people cave their knees because they favor their posterior and try to use it to get out of the hole when they should keep the hips under the bar. It's possible that the lifter needs to relearn the movement. Still, if this is happening at maximal or near-maximal weights, I wouldn't worry about it; many very proficient lifters in history did this and there's no issue.
Lastly, heaving snatch balances and snatch balances will help with the lifter's turnover. Personally, I think snatch balances are a little easier because you can move your feet, so it may be helpful to start there and then move into your heaving snatch balances. Either way, both will help. Tall/dip/high-hang snatches will also force the lifter to be quicker under the bar, so these are things you can use during warm up to help build muscle memory before heavier lifts.
Hope this helps,
Javier A. Sanjuan
Olympus Barbell Club
Dear God, please help me lift heavy and be awesome. Thanks. Amen.