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I’d suggest not using the default DNS name that AWS provides for the server. Purchase a domain name (or create a subdomain for a domain you already own/manage) and point it at the server. Then purchase the SSL cert for that DNS name (where you are the domain admin). Make sure all clients are connecting to the new name so that the cert will match.
The AWS Route 53 service is great for this if you don’t already manage DNS elsewhere.
To put something into the root of your domain for verification you can do that with IIS Manager on your AWS server. If you turned on web publishing it will be enabled. Go to IIS Manager and open up the site on the left. Click on the Sites folder then right click on FMWebSite and click on explore and add the file that your SSL provider wants you to in the folder that opens up.
You will want to register the Domain your clients are using for the SSL. For example I have added a DNS entry (A-Name) filemakerserver.schwarzsoftware.com.au and pointed that to an elastic ip address. Clients only connect to filemakerserver.schwarzsoftware.com.au and the SSL is registered for that DNS so the SSL works fine for the clients. If you don't do that your clients will get an invalid SSL error.
Greg and Carl:
Thank you very much!
Excellent input, I will try these approaches soon and let you know the result.