Hi,
Have you changed the settings of the CRM website a lot from when it was installed from within IIS? and did it work previously or has it always been broken? I know that, for instance trying to add website bindings from the IIS especially to HTTPS, may brake the installation. These kínds of settings have to be made from the deplyment manager which then writes to IIS. I am not saying that you have done any of these, I am just giving you a heads up in case you are close.
You can Always take a backup of the database, restore it in a lab Environment and then do your test installations there. Preferably in virtual Environments where you can use snapshots to easily revert.
Maybe I have given you some ideas or ways forward anyway. Good luck!