Published .NET app is looking for API in source folder - c#

I'm new to API development and have created a Web API app that works fine locally (Visual Studio / IIS Express). When I publish and deploy to IIS 8.5, the HTML pages work fine, but when I make an ajax call to my APIs, I get a 500 error. It somehow seems to be looking at my source code folder on my c: drive!, instead of the dll.
I'm guessing I botched something in the VS Publish setting, or in my API routing in WebApiConfig.
Any idea on why it's looking in my source directory?

From what I can understand, is that your API is expecting custom header as part of your request. Please use PostMan or any other REST API Client to test your API by adding required headers. If you build and publish in release mode you will not find your local source code folder path.

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But I am trying to publish it on my local IIS.
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What would be deployed depends on your project's file structure.
If your web app runs successfully, don't mind about the content in wwwroot. If not, make sure your project could run successfully local, then deploy follow this tutorial: Quickstart: Deploy an ASP.NET web app
It turns out that the web app will 404 on lots of types of errors, in this case a problem connecting to the database. I was able to figure it out using Diagnostic Tools and the application error logs, so would recommend anyone else having unexplained 404s to check the logs. Pretty basic stuff, but as I said this is all new to me.

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some pages do not display after deploying

I have a perfectly running asp.net c# application, i have windows 7, vs200, vs2010 and sqlserver2008r2 installed on my computer. I use vs2008 for my application. I use web deploy in release mode to generate a package and send it to an administrator to deploy the pack on a testing server. the deployed application works fine for some aspx pages but for some others pages it doesn't find them and displays an error message:
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thank's for the help
ps: i do not have access or control over the testing server. the application was working fine before my first deploy.
The best explanation is that pagename.aspx isn't at the expected location.
Check if the file is there
If so, check if iis has the right directory for you webapplication
If not, make a correct deployment (do a test deployment on an clean directory).
Another hypothesis: It can happen if you are using svn and forgot to add unversion files to subversion.

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