Did you tried by opening command prompt "Run As Administrator"?
Access denied error comes if local user doesn't have permissions to delete files as obovious. You can skip the cleanup part and do it manually in case command line is causing permission issues.
After amps are installled you need to make sure you delete the exploded war files "alfresco" and "share". Once tomcat restarts the war files will explode again with the applied amps.
I think you did not delete the exploded wars that's why you can't see the module as you mentioned.
Did you also tried installing any other amps to confirm the same whether it is just the pdf-toolkit or local permission issue only.
Alternatively you can also copy the repository amp to <YourAlfrescoInstallationPath>/amps and share amp to <YourAlfrescoInstallationPath>/amps_share
and use the utility 'apply_amps.bat' that comes with out of the box installation to install amps. some details can be found here as well: https://javaworld-abhinav.blogspot.com/2022/05/setup-acs-7-ass-2-and-local-windows.html#apply-amps-a...
~Abhinav
(ACSCE, AWS SAA, Azure Admin)
