Looks like you started a pretty good thread man! I very much enjoyed reading through it!
At the end of the day every machine has it's place. Personally, I don't use the smith machine for squats. Some smith machines are on an angle and some are completely verticle, but either way my body doesn't necessarily follow the same path on every squat. Also, if your neck is sore, it is probably from the force of lifting the weight combined with possible friction from pushing the bar against the rods of the smith machine.
@Erica_Stibich however does use the smith machine for squats, but because she is using the smith machine she is taking advantage of the bar being in place and puts her feet further forward. Traditional squats bother her lower back and with the smith machine she can go deeper and heavier on squats while continuing to work on her flexibility.
Keep us posts on your results and if you need more help with your deadlift, I have a really great article full of photos and videos right here for you to check out!
DEADLIFT: Why you‘re not lifting as much weight as you could.
Have a great week!