When I finished the restoration my rear right hand side was way lower than the rear left, a good 10 cm lower on the right.
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I adjusted the Right hand side to level the rear but in order to achieve this the adjusting ring on the right had to be 6 cm higher than the ring on the left. But surely my right rear spring is now under more load that the left so the car will be out of balance. Really puzzled why one side sits higher than the other.
To get my head around this, where are you measuring your original 10cm from, the body wheel arch centre, underneath the sill at the front of the wheel arch or from some point on the chassis ? Being old school and mentally converting that to inches, it sounds a heck of a lot out to me even if the body wasn't mounted squarely on the chassis. If the chassis was 10cm out on the chassis legs where the damper crossmember bracket mounts then I think it would be very obvious and probably wouldn't go together easily.
The second point, again, 6cm difference again comes to me as a lot. My kit is the same as yours with just different spring rates and the difference side to side is very little. When I adjusted mine I would roll the car back & forwards to settle it between checks. Then I'd drive it round the block and do it all again because they do change a bit after you've driven them on our bumpy roads.
Going back to the 6cm thing, how much additional load you have there depends on what the free length of the spring is to start with. When I was researching my springs I found a survey from Phil Ethier (Yahoo group) for the S2 which gave a lot of detail. I've attached a screenshot here and you can see that if you have standard springs then according to his data you have roughly 400lbs static and helpfully he gives plenty of dimensions you can check against.
If you've ramped up one side by another 6cm and still got the same overall damper mount dimensions (bush to bush centres) there's going to be something like 180lbs extra on one side (75lbs/inch compression rate). That sounds a lot to me and it's beyond my experience/reasoning.
If there's no obvious physical reason for the disparity (bent chassis/crossmember damper mountings/etc) then I'd start with the springs. You can calculate the approx rate from the formula in the second attachment and should be able to get the dimensions with a digital vernier without dismantling the assembly. I can't see how on earth you'd get a mismatched pair of springs but I'd want to rule it out before going further.
Any chance of a photo of the suspension from underneath when it's on it's wheels ?