Ya the smith machine is a totally different movement all together. Don't bother. As for your neck pain, I agree it could be you're leaning forward too much at the bottom. Possibly cause you're ROM isn't quite there and you're simulating depth by leaning forward. These are all guesses btw, but I think it makes somewhat of sense.

Not to hijack but I've been experiencing mild numbness lately in my hands/arms after I squat.... wtf..