assistance with mongodb setup on windows server
You shouldn't scan the folder in which mongodb stores it's data files, as this will degrade performance. The location is set by using the --dbpath C:\Where\You\Want\The\Files flag at runtime. 

With regards to best practices for clustering, I'd recommend taking a look at the Infrastructure Requirements for a Sharded Cluster page.

At a minimum, you will need three config servers, two or more shards and one or more MongoSes