I encountered this same issue on my Zilla.
I swapped out the knob-side spring for a shorter one and it gave me a little extra length in the shooter. There are rods that are a quarter inch longer, but you kind of have to stumble into them on your travels.
As for centering, you will have to remove the two red machine screws that anchor the backing plate of the shooter housing, loosen the three mounting screws just enough to allow you to reposition the housing, then lower the playfield and test plunge until you have the housing in just the right spot.
Lastly, raise the playfield a final time and torque the mounting screws.
Remember, this playfield has a plunge lane that is bi-level! It is very prone to rattley plunges!!