Hey Jazzy
Aren't the scale lengths and body shapes different on your two Series basses? If so that may account for the difference in pickup placement and contribute to the sonic differences though I imagine the neck lams have a huge impact, too.
Which leads to a general question (probably for Mica). Would the pickup placement of two Series basses, one a Series I and one a Series II, be different if the instruments shared the same body shape and scale length?