Hi Ron, the Bilstein is a different shaft size than the Koni as you noticed. I have always had the issue that the Koni was too small for my camber plates and I had to use a bushing for the mono ball at the top of the camber plate. There must be two different monoball inner ID sizes.
Pull the monoball out of the camber plate and measure it. Look at mcMaster Carr online and see if the make the correct one. Here is the link
www.mcmaster.com/#standard-spherical-swivel-bearings/=nvs2gg
As far as the rear shocks go I have never done anything to mine. I did not know that the bump stop rubber was removable.
If the car is too low it will cause problems with handling.