I've seen the error message before, but it was related to sce_module issues with backup games, not with installing homebrew...are you able to install the VitaShell VPK? You can try using that to install VPKs, and if that still doesn't work you can extract the VPKs using 7zip or Winrar (since they're basically normal .zip files) and then transfer the folder and install it that way on the newest VitaShell version.
That happens because there are no more Henkaku Beta's anymore, Taihen has been officially releases as of the 27th of Dec. That shouldn't be the cause at all, and if it were then resetting the configuration should've fixed it.