I went through the steps of manually recreating the Web Applications and default Sharepoint websites by following:
To recreate the original internal Web site environment
http://technet.microsoft.com/en-us/library/dd560621(v=ws.10).aspx
Obviously I've made a mistake along the way and either the name or the url for the sharepoint has ended up assites not remote.domain. This is now causing issues with the certificates for all web application services including Exchange client access via Outlook. Using the self issues certificate of remote.domain users receive an error stating the name on the certificate is wrong as it's connecting to "sites" not "remote.domain". As a work around I've found that if I set the certificate to the sites certificate that was maybe created during my attempted fix or already existed the errors stop. But then using autodiscover to setup Outlook (which I have also setup/fixed) gives an error because it's expecting the cert to say remote.domain as per the autodiscover record.
Below is a screenshot from the Web Applications under Sharepoint Administration.
Below is screenshot of sites as binding in IIS for SBS Web Applications. Not sure if this part matters.
So help in getting this sorted would be much appreciated.