When I try to access my server via the EC2 dns, it resolved to my domain name, why is that? - The only thing I've done is setting up Route53 with CNAME and Alias. I don't have any redirect in IIS whatsoever.
If Route53 does that, ELB won't be able to access the file health checking on the instance because it tries to get it using the Instance DNS.
Furthermore, ELB returns "Status: 0 of 1 instances in service" all the time now. I think that because of the resolvement, it just can't read the file on the EC2 instance.