The files downloaded by the Magento Connect Manager are stored in the following directories:
To fix the issue with Magento Connect, you can delete the downloader/pearlib/pear.ini file, then try again. It will re-generate the PEAR paths.
The temporary data goes to the directories you listed. The files actually go here:
Deleting just the pear.ini file doesn’t always work either, there’s still many other files that reference the absolute path (assuming that is the problem). Best to just write down the list of third-party extensions you have installed and replace the downloader directory with a default one: