Type added through AddType is not checked for compression. Only globally defined types are. It does not hurt anything by adding the type globally.
We will address this issue later.
PHP install some libraries like PEAR into the installation directory, if you remove it, the lsphp binary you built may not work properly if any library is used.
cpanel 11 update probably turned on apache automatically. Also, make sure the "httpd" service is unchecked.
For deleting /tmp/lshttpd, you can modify /etc/init.d/lsws
Have you configured LSWS to download the update package for you? maybe for some reason the download failed, just update it manually from command line, and see if next release will go through.