Thank you Tony, I was able to create a new Enterprise application with a web module and deploy it successfully to my server - I used the same profile in fact. It installed and ran fine. So I believe the basic installation of WebSphere is good. Here is the deployment log.
MyEclipse: deployment START exploded project: TestProject server: websphere85Server#AppSrv01 time: Mon Sep 10 11:27:24 EDT 2012
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WASX7357I: By request, this scripting client is not connected to any server process. Certain configuration and application operations will be available in local mode.
WASX7303I: The following options are passed to the scripting environment and are available as arguments that are stored in the argv variable: "[D:\Program Files\IBM\WebSphere\AppServer\profiles\AppSrv01\installableApps\TestProject.ear, CNWIN168QXNode01Cell, CNWIN168QXNode01, server1, TestProject, {{"TestProjectWeb.war" "TestProjectWeb.war,WEB-INF/web.xml" default_host}}, {{.* .* AppDeploymentOption.Yes 1}}, false, false, true, D:/Program Files/MyEclipse Blue Edition/MyEclipse Blue Edition 10/configuration/org.eclipse.osgi/bundles/20/1/.cp/scriptutil/scriptutil.jar, none, 1.4, true, none]"
D:\Program Files\IBM\WebSphere\AppServer\profiles\AppSrv01\installableApps\TestProject.ear
CNWIN168QXNode01Cell
CNWIN168QXNode01
server1
TestProject
{"TestProjectWeb.war" "TestProjectWeb.war,WEB-INF/web.xml" default_host}
{.* .* AppDeploymentOption.Yes 1}
-nopreCompileJSPs -distributeApp -server "server1" -useMetaDataFromBinary -nodeployejb -appname "TestProject" -createMBeansForResources -reloadEnabled -reloadInterval 1 -deployws -validateinstall off -processEmbeddedConfig -filepermission .*.dll=755#.*.so=755#.*.a=755#.*.sl=755 -buildVersion Unknown -noallowDispatchRemoteInclude -noallowServiceRemoteInclude -MapWebModToVH {{"TestProjectWeb.war" "TestProjectWeb.war,WEB-INF/web.xml" default_host}} -JSPReloadForWebMod {{.* .* AppDeploymentOption.Yes 1}}
false
false
true
D:/Program Files/MyEclipse Blue Edition/MyEclipse Blue Edition 10/configuration/org.eclipse.osgi/bundles/20/1/.cp/scriptutil/scriptutil.jar
-nodeployejb
1.4
-processEmbeddedConfig
ADMA5016I: Installation of TestProject started.
ADMA5058I: Application and module versions are validated with versions of deployment targets.
WSWS0041I: Web services deploy task completed successfully.
ADMA5005I: The application TestProject is configured in the WebSphere Application Server repository.
ADMA5005I: The application TestProject is configured in the WebSphere Application Server repository.
ADMA5081I: The bootstrap address for client module is configured in the WebSphere Application Server repository.
ADMA5053I: The library references for the installed optional package are created.
ADMA5005I: The application TestProject is configured in the WebSphere Application Server repository.
ADMA5001I: The application binaries are saved in D:\Program Files\IBM\WebSphere\AppServer\profiles\AppSrv01\wstemp\Script139b0cae506\workspace\cells\CNWIN168QXNode01Cell\applications\TestProject.ear\TestProject.ear
ADMA5005I: The application TestProject is configured in the WebSphere Application Server repository.
SECJ0400I: Successfully updated the application TestProject with the appContextIDForSecurity information.
ADMA5005I: The application TestProject is configured in the WebSphere Application Server repository.
ADMA5005I: The application TestProject is configured in the WebSphere Application Server repository.
ADMA5113I: Activation plan created successfully.
ADMA5011I: The cleanup of the temp directory for application TestProject is complete.
ADMA5013I: Application TestProject installed successfully.
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In trying to bring over our 6.1 project I essentially copied the workspace, deleted all previous server references, compiled and replaced a few references. I am thinking now perhaps I should recreate the project in the tool instead of working off an old workspace. I do not have both WebSphere 6.1 and 8.5 installed on the machine I am trying this on so I can't attempt to redeploy back to 6.1 on this machine. In comparing the deployment descriptor and application.XML files, I see no difference.
New Ones
#Web XML
<?xml version="1.0" encoding="UTF-8"?>
<web-app version="2.5"
xmlns="http://java.sun.com/xml/ns/javaee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://java.sun.com/xml/ns/javaee
http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd">
<display-name></display-name>
<welcome-file-list>
<welcome-file>index.jsp</welcome-file>
</welcome-file-list>
</web-app>
#Application.xml
<?xml version="1.0" encoding="UTF-8"?>
<application xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="5"
xsi:schemaLocation="http://java.sun.com/xml/ns/javaee
http://java.sun.com/xml/ns/javaee/application_5.xsd"><description></description>
<display-name>TestProject</display-name>
<icon></icon><module id="myeclipse.1347290516079">
<web>
<web-uri>TestProjectWeb.war</web-uri>
<context-root>/TestProjectWeb</context-root>
</web>
</module>
</application>
Top of my project descriptor
<?xml version="1.0" encoding="UTF-8"?>
<web-app version="2.5"
xmlns="http://java.sun.com/xml/ns/javaee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://java.sun.com/xml/ns/javaee
http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd">
<display-name>SupplierNetRelease</display-name>
I am afraid a few jars I had to bring in may be incompatible so will be trying to recreate the workspace from scratch. Does that sound reasonable?