Bottoming out the shocks should simply not happen EVER The bump stops in the air springs (or the bump stops on the leaf springs) should be encountered before the shocks bottom out. You should check that the springs (air or leaf) are adequately supporting the vehicle, BUT I think in your situation, you have installed shocks that are too long for your application. I have heard from others the difficulty in finding the correct length Koni shocks to fit a particular chassis. Good luck with your research, but I would think that the shocks are definitely your problem.
Richard