Why oh why didn't he fork php/php-src, make a branch for his changes, then commit as he went along? This just ends up as a big patchbomb. They're never going to merge his changes, and I don't blame them.
In this case, it would be better to maintain it as several topic branches (so that each logical change can be implemented in as many patches as necessary), and then a good old octopus merge as "master" that you force-update every so often.
(Yes, everyone hates you for modifying published history, it's evil, it will give you bad breath, yeah yeah yeah. But you have to think of this use case as a "code wiki" rather than "list of changes leading to the current state". After the patches are accepted, then don't force update them. When they are still in flux, modify history as often as necessary to make your changes easily comprehensible.)
His work is based off 5.3.x, there is probably a branch for it in the official SVN repo. As one commenter noted, the github mirror is stale so he'd need to fork it and then update it with the official svn to find the branch.
It may make sense to rebase it off of trunk of svn.
master would always contain the php-base+the octopus merge. So if the php-base was 5.3.6, it would be 5.3.6+patches. Tomorrow PHP 5.3.7 comes out, and then master would be 5.3.7+patches.
EDIT - Hopefully we can straighten this around: https://github.com/infusion/PHP/commit/790d551ac9ef8e204b44f...