I've found doing the custom install works best especially if you don't have a need for the other website templates. If you have an Ultimate license, I'd suggest not removing any modules as I've found some are dependent on others and it does cause some problems. This could be the issue you're having, IIS trying to compile something that doesn't exist and causes errors. Check out the server event log.
Also, what's your server setup? Do you have at least 2 CPU's? Found that works best.