Reference this MSDN article on performing a clean IIS reinstall: https://blogs.msdn.microsoft.com/friis/2017/01/16/how-to-perform-a-clean-reinstallation-of-iis/
Please reference the user guide and/or release notes relevant to the App Control Server version that is being reinstalled
If the DefaultAppPool is crashing check the Application Event Viewer for possible errors to determine specific cause similar to this article