This is several months late but might help someone in the future. From the two web.configs I notice you went from an InProcess to OutOfProcess hosting model.
I did the same thing and got a very similar result. For me it threw the error waiting for database data. I found this article helped (though is sort of the reverse of what I was doing): ASP.NET Core Request Timeout IIS In-Process Mode - The Seeley Coder
Essentially I set the timeout to 30min
<aspNetCore processPath="dotnet" arguments="[app name].dll" stdoutLogEnabled="false" stdoutLogFile="[log location]" hostingModel="OutOfProcess" requestTimeout="00:30:00"/>
and just to make sure added
<httpRuntime executionTimeout="1800" />
to the web.config Hope this is of some use to somebody.