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Perhaps start phalcon 1.3 and 2.0 on the same server VDS?
ngnix + php-fpm
you have to be running diffrent php version per host ( like I do )
so your koko.com will be runing /myphp/php-5613/ and
your toto.com will be running /myphp/php-5613-with-phalcon-1.3 ( as an exmaple )
a tip can be fond here :
make && sudo make install