Hi,
Based on my experience, there is not big difference in performance between ASP.NET website and ASP.NET web application when we deploy them on server with same configuration.
In this case, please try to use Publish utility (Right click project name in Solution Window and select "Publish.." for web application or "Publish Web Site" for website project) to precompile them and then deploy them on server.
Besides, we also need to make sure the web.config setting is same, such as debug mode in compilation section.
I look forward to receiving your test results.