ClickOnce deployment in VB.NET - launch online only error - vb.net

Question

I have been trying to fix this problem for a long time. When I fix one issue another one pops up. I am pretty sure I am on the last hurdle though.
I have an application I want to make available to users online. A click launches it, and it downloads and runs from the download cache. This is an option in Visual Studio 2010 ClickOnce deployment.
When I first uploaded the files through FTP to the webserver I had issues with the file extensions, the webserver was not recognizing them. I was able to add the correct MIME types to the htaccess file and, success, the application almost launches..
I am getting the same application cannot be started error with the details below,
PLATFORM VERSION INFO
Windows : 6.1.7601.65536 (Win32NT)
Common Language Runtime : 4.0.30319.296
System.Deployment.dll : 4.0.30319.1 (RTMRel.030319-0100)
clr.dll : 4.0.30319.296 (RTMGDR.030319-2900)
dfdll.dll : 4.0.30319.1 (RTMRel.030319-0100)
dfshim.dll : 4.0.31106.0 (Main.031106-0000)
SOURCE
Deployment url : http://apps4you.comyr.com/appTest8 /Application%20Files/snake_1_0_0_6/snake.application
Server : Apache
IDENTITIES
Deployment Identity : snake.application, Version=1.0.0.6, Culture=neutral, PublicKeyToken=5bd57d3abffa2377, processorArchitecture=x86
APPLICATION SUMMARY
* Online only application.
* Trust url parameter is set.
ERROR SUMMARY
Below is a summary of the errors, details of these errors are listed later in the log.
* Activation of http://apps4you.comyr.com/appTest8/Application%20Files/snake_1_0_0_6/snake.application resulted in exception. Following failure messages were detected:
+ The remote server returned an error: (500) Internal Server Error.
COMPONENT STORE TRANSACTION FAILURE SUMMARY
No transaction error was detected.
WARNINGS
There were no warnings during this operation.
OPERATION PROGRESS STATUS
* [27/04/2013 2:29:49 p.m.] : Activation of http://apps4you.comyr.com/appTest8/Application%20Files/snake_1_0_0_6/snake.application has started.
* [27/04/2013 2:29:50 p.m.] : Processing of deployment manifest has successfully completed.
* [27/04/2013 2:29:50 p.m.] : Installation of the application has started.
ERROR DETAILS
Following errors were detected during this operation.
* [27/04/2013 2:30:07 p.m.] System.Net.WebException
- The remote server returned an error: (500) Internal Server Error.
- Source: System
- Stack trace:
at System.Net.HttpWebRequest.GetResponse()
at System.Xml.XmlDownloadManager.GetNonFileStream(Uri uri, ICredentials credentials, IWebProxy proxy, RequestCachePolicy cachePolicy)
at System.Xml.XmlUrlResolver.GetEntity(Uri absoluteUri, String role, Type ofObjectToReturn)
at System.Xml.XmlTextReaderImpl.OpenAndPush(Uri uri)
at System.Xml.XmlTextReaderImpl.PushExternalEntityOrSubset(String publicId, String systemId, String baseUriStr, Uri& baseUri, String entityName)
at System.Xml.XmlTextReaderImpl.DtdParserProxy_PushExternalSubset(String systemId, String publicId)
at System.Xml.DtdParser.ParseExternalSubset()
at System.Xml.DtdParser.Parse(Boolean saveInternalSubset)
at System.Xml.DtdParser.System.Xml.IDtdParser.ParseInternalDtd(IDtdParserAdapter adapter, Boolean saveInternalSubset)
at System.Xml.XmlTextReaderImpl.ParseDtd()
at System.Xml.XmlTextReaderImpl.ParseDoctypeDecl()
at System.Xml.XmlTextReaderImpl.ParseDocumentContent()
at System.Deployment.Application.ManifestValidatingReader.XmlFilteredReader.Read()
at System.Xml.XmlCharCheckingReader.Read()
at System.Xml.XsdValidatingReader.Read()
at System.Deployment.Application.ManifestReader.FromDocument(String localPath, ManifestType manifestType, Uri sourceUri)
at System.Deployment.Application.DownloadManager.DownloadApplicationManifest(AssemblyManifest deploymentManifest, String targetDir, Uri deploymentUri, IDownloadNotification notification, DownloadOptions options, Uri& appSourceUri, String& appManifestPath)
at System.Deployment.Application.DownloadManager.DownloadApplicationManifest(AssemblyManifest deploymentManifest, String targetDir, Uri deploymentUri, Uri& appSourceUri, String& appManifestPath)
at System.Deployment.Application.ApplicationActivator.DownloadApplication(SubscriptionState subState, ActivationDescription actDesc, Int64 transactionId, TempDirectory& downloadTemp)
at System.Deployment.Application.ApplicationActivator.InstallApplication(SubscriptionState& subState, ActivationDescription actDesc)
at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivation(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl)
at System.Deployment.Application.ApplicationActivator.ActivateDeploymentWorker(Object state)
COMPONENT STORE TRANSACTION DETAILS
No transaction information is available.
So the launch of the application is looking promising, but it's still not there. What could this internal server error (500) be? I have done some research, and it seems pretty generic. What do the details in the stack trace mean?