Confluence 5.4 Upgrade Issues

 I am trying to upgrade confluence from 4.1.6 to 5.4 and my upgrade was successful in the logs. After upgrade, I am able to login to new confluence 5.4 and I see all the spaces and pages on the left pane(Documentation Theme). I searched all spaces and tried mulple pages but there was no page content displayed on the right side pane. I see the following warning message in the log file.
2014-02-11 17:34:35,384 INFO [main] [atlassian.plugin.manager.DefaultPluginManager] init Initialising the plugin system
2014-02-11 17:34:57,143 WARN [main] [factory.transform.stage.GenerateManifestStage] assertSpringAvailableIfRequired The Spring Manifest header in jar 'activeobjects-confluence-spi-0.24-m5-confluence.jar' isn't set for a 300 second timeout waiting for  dependencies.  Please add ';timeout:=300'
2014-02-11 17:35:00,942 WARN [main] [factory.transform.stage.GenerateManifestStage] assertSpringAvailableIfRequired The Spring Manifest header in jar 'applinks-plugin-4.0.11.jar' isn't set for a 300 second timeout waiting for  dependencies.  Please add ';timeout:=300'
2014-02-11 17:35:01,465 WARN [main] [factory.transform.stage.GenerateManifestStage] assertSpringAvailableIfRequired The Spring Manifest header in jar 'atlassian-failure-cache-plugin-0.6.jar' isn't set for a 300 second timeout waiting for  dependencies.  Please add ';timeout:=300'
2014-02-11 17:35:08,692 WARN [main] [factory.transform.stage.GenerateManifestStage] assertSpringAvailableIfRequired The Spring Manifest header in jar 'atlassian-pretty-urls-plugin-1.5.jar' isn't set for a 300 second timeout waiting for  dependencies.  Please add ';timeout:=300'
2014-02-11 17:35:09,669 WARN [main] [factory.transform.stage.GenerateManifestStage] assertSpringAvailableIfRequired The Spring Manifest header in jar 'atlassian-rest-module-2.8.0-m7.jar' isn't set for a 300 second timeout waiting for  dependencies.  Please add ';timeout:=300'
2014-02-11 17:35:10,546 WARN [main] [factory.transform.stage.GenerateManifestStage] assertSpringAvailableIfRequired The Spring Manifest header in jar 'atlassian-template-renderer-api-1.4.3.jar' isn't set for a 300 second timeout waiting for  dependencies.  Please add ';timeout:=300'
2014-02-11 17:35:11,142 WARN [main] [factory.transform.stage.GenerateManifestStage] assertSpringAvailableIfRequired The Spring Manifest header in jar 'atlassian-template-renderer-velocity16-plugin-1.4.3.jar' isn't set for a 300 second timeout waiting for  dependencies.  Please add ';timeout:=300'
2014-02-11 17:35:12,846 WARN [main] [factory.transform.stage.ScanDescriptorForHostClassesStage] execute The plugin 'atlassian-universal-plugin-manager-plugin-2.14.jar' uses a package 'org.apache.commons.fileupload.servlet' that is also exported by the application.  It is highly recommended that the plugin use its own packages.
2014-02-11 17:35:13,953 WARN [main] [factory.transform.stage.GenerateManifestStage] assertSpringAvailableIfRequired The Spring Manifest header in jar 'atlassian-webhooks-plugin-0.17.3.jar' isn't set for a 300 second timeout waiting for  dependencies.  Please add ';timeout:=300'
2014-02-11 17:35:33,498 WARN [main] [factory.transform.stage.GenerateManifestStage] assertSpringAvailableIfRequired The Spring Manifest header in jar 'confluence-sal-plugin-5.4.2.jar' isn't set for a 300 second timeout waiting for  dependencies.  Please add ';timeout:=300'
2014-02-11 17:35:35,368 WARN [main] [factory.transform.stage.GenerateManifestStage] assertSpringAvailableIfRequired The Spring Manifest header in jar 'confluence-tdm-merger-5.4.2.jar' isn't set for a 300 second timeout waiting for  dependencies.  Please add ';timeout:=300'
2014-02-11 17:35:49,227 WARN [main] [factory.transform.stage.GenerateManifestStage] assertSpringAvailableIfRequired The Spring Manifest header in jar '1392159132000support-core-1.2.4.jar' isn't set for a 300 second timeout waiting for  dependencies.  Please add ';timeout:=300'
2014-02-11 17:35:51,283 WARN [main] [factory.transform.stage.GenerateManifestStage] assertSpringAvailableIfRequired The Spring Manifest header in jar '1392159132000supplier-core-1.0.6.jar' isn't set for a 300 second timeout waiting for  dependencies.  Please add ';timeout:=300'

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This widget could not be displayed.

This is just blocks of log that I can't really read. Could you tidy it up and explain the problem?

I am trying to upgrade confluence from 4.1.6 to 5.4.2 and my upgrade was successful in the logs. After upgrade, I am able to login to new confluence 5.4 and I see all the spaces and pages on the left pane(Documentation Theme). I searched all spaces and tried mulple pages but there was no page content displayed on the right side pane. There are no specific error messages in the log file. I followed the below KB article flushed the plugin cache and restarted confluence.. The timeout logs are not shown but the page contents in all spaces are not coming up.. None of the page links are missed as I am able to see all the links in the left pane but when i click on the link to load a page, the page is rendering blank with page title on the top..

https://confluence.atlassian.com/display/CONFKB/Plugins+are+Disabled+at+Startup+and+Various+Timeout+Errors+Appear+in+the+Logs+After+Startup

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