We were able to resolve the url problem by:

1. commenting out the following lines in the web.config (It's already configured at the server level):

<defaultDocument>
      <files>
        <remove value="Default.aspx"/>
        <add value="Default.aspx"/>
      </files>
    </defaultDocument>

2. Resetting the Application pool.

The ul is working fine now e.g. www.mysite.ie  brings up the home page. 

Is commenting out this line OK?  I just want to make sure that this will not cause any issue with the site.  The site seems to working ok except for the help opening up in a separate page as discussed previously.

Hi Joe,

I was finally dealing with the ISP's senior engineer and here is his explanation:

"You need to remove the default document details from the web.config file, this is handled from the control panel and you already have it set in the control panel.

Remove the content below from the web.config file and you should have no problems".

Well, he was correct, except it does not take effect until the application pool is reset.  Before reset 500 error on all Url's, I could not access the site at all,  after reset,  perfect.

Looks like we finally made over the finish line, albeit, about a week after we started.   I think this was the longest it has ever taken me to get a site up.. but I learned a few things.

Big thanks to you and Asad for all your support. 

Hopefully this thread might help others who might come across similar configuration issues, especially if using Blacknight shared hosting.