So after fitting a set of rear reverse cones to my 90 to stop the springs moving, when putting her back down on the wheels I noticed that the car is now slightly lower on side than the other,

I 've checked the springs are all fitted correctly but I've got about 20/30mm lower passenger side rear quarter than the divers, no obvious leaky damper or anything.

What am I missing or what should I check.

Have you moved the motor ? . Normally giving it a small drive will make it level
Or spring upside down

no, not drive her since