The spring for the mixture screw won't have any bearing on what goes to the motor - it simply applies pressure on the screw so it stays where you want it. If they were overly long they could bottom out before the tip does, giving a false setting at, say, 1 1/2 turns out, but you don't reach ideal mixture setting based on the position of the screw; that comes from fine tuning.
Carb work needs to be very methodical. As you've discovered, you think you've done everything thoroughly but anything missed will create woes later. Good that you've on the right track.