The Pro S should not clunk when installed correctly. You most certainly should be using all 4 bumpstops as they are designed to prevent the dampeners from compressing further than they should. Removing the bumpstops can result in damage to the dampeners (as well as a voided warranty.)
I would recommend going through the installation again, paying particular attention to the upper mount assemblies.
Email
BrianN@Skunk2.com and I will provide the most up to date version of the installation instructions for your review. If you would like to attach pictures I will be happy to try and troubleshoot your problem.
Skunk2 also runs an online HelpDesk through
www.skunk2.com. Customers are welcome to post questions on that HelpDesk free of charge. We constantly check that HelpDesk so expect a response quickly.