So it sounds like you're still having some issues. You should be able to point IIS to your previous copy of the file system, with the web.config pointing to the previous copy of the database. Make sure the web site properties are configured correctly. You may want to try deleting the existing web site in IIS and create a new one.

As far as the clean install goes, I would bring down a new copy of the install package for 4.9. Extract the files and give the appropriate permissions. Create a new database and point the web.config to the new database. Create a new website in IIS and point to the newly extracted files. It has worked thousands of times, just have to figure out what part is missing.