Yes its lowered 40mm. On 'recoil' custom wound springs. They sit really tight in the cups when its jacked up so that is why i havent a clue how they had mislocated.
You have 3 options. you can use a strap that bolts to your subframe and then to the floor plan above it, ie a length of seat belt. this will then stop the subframe from dropping to far once jacked up. This is a common thing done to lowered cars.
Other options include new custom wound springs or getting metal p clips and screwing the tops and bottoms of the springs to there cups.
The headlight alighnment is easy, it is just 2 screw adjusters on the light fronts that you can adjust once the lights are up.
I put my car next to Dr silvias s12 infront of a wall at night and matched the headlight heights to his on the wall