I think your best bet here is to hook into the flow at the time of uploading and processing the uploaded file.
There is a filter (line 327, file.php):
apply_filters( 'wp_handle_upload', array( 'file' => $new_file, 'url' => $url, 'type' => $type ), 'upload' );
You could create a filter within which you do nothing else but create a global variables to hold the current values for:
wp_get_themes();
wp_get_plugins();
then, within your existing functions
HandleThemeUpload() { }
HandlePluginUpload() { }
you get the themes and plugins again and then compare these results with your previous global results using array_diff(): e.g.
$NewPlugin = array_diff( $LatestPlugins, $OldGlobalPlugins );
Then you have the new plugins / themes.
Hope that helps.