The spring will be on the perch which is seated in the control arm. pulling your fenders all depends on your wheels. if you're running alphards you don't need to pull them, just adjust the camber until it doesn't rub
In that pic I had 215/35/18's up front and 215/40/18's out back. FK coilovers without helper springs, probably around 5 threads from the bottom, rear coils all the way down with both locking collars removed.
Frame was not notched. I ran the car with the axle banging for a very long time without any real negative impact to the car.
A skidplate will not allow for a very low ride height, unless you can find one that is pretty much flat and sits exactly as the plastic under the car already does.