How to get SSL working

Assuming the website is written in ASP.NET, you can play around the web.config file by extending the 'executionTimeout' value (i.e. <httpRuntime executionTimeout=""> section in <system.web>).

It would also be good to setup a redirect from http to https (done in web.config, using URL Rewrite module in IIS), or the same can be done with HTTP Redirect in IIS.

Concerning your last bullet point - it doesn't matter if you use subdomains, as a rule, they all should be registered within Comodo (or whatever provider you use).

Returning to the main question, it is hard to say what may go wrong. There is a tool for IIS 7 SSL diagnostics. It will provide you a detailed report of SSL settings. Please use it to determine what's wrong with your settings: https://blogs.msdn.microsoft.com/vijaysk/2009/09/20/ssl-diagnostics-tool-for-iis-7/

And the last - bear in mind that opening ports in Windows Server Firewall is not enough, as VM in Azure uses it's own networking settings (network security group). You may need to configure the endpoints to make those ports available to the external world. Have a look at 'Networking' blade in VM settings. That could be the reason ;)