This sounds you are just asking for problems.
1) Authority stealing - What exactly do you mean by this? If you write your Web Application the correct way, then it will only be able to do things your client allows, find out what sort of configuration they are using.
2) Read files with sensitive data - I suggest you don't attempt to do this. Your web application should not be on a computer with sensitive data if its accesible to the internet.
3) Software tweaking - Say What?
4) Any security issues - This is not possible. Considering you are even asking how to prevent this, means you will have security issues, even Microsoft has security issues.
Encrypting the Web.Config only protects the contents within it, if there is nothing senistive within it, it really serves no purpose to encrypt it.
It sounds you are way over your head.