--The version of Squid included in this appliance VM is: 3.1.19-1ubuntu3.12.04.2 ; however, if you want to uninstall the .deb package and reinstall from source, there should be very few issues beyond possibly changing some directory paths.
http://www.squid-cache.org/Versions/v3/3.3/
http://arfanahmedcheema.blogspot.com/2013/04/squid-333-compilation-on-ubuntu-12.html
--As far as configuring for transparent proxy:
http://tuxnetworks.blogspot.com/2012/07/squid-3-transparent-proxy.html