nice post, but it misses out the bit about documenting the change, making sure that your distribution doesn't suddenly nuke your changes when it does an upgrade, finding programmers who can work on your codebase given your customisation of php...
It's a useful post, but I'd like a but more warning that you really don't want to do this unless your proposing on either contributing this back into the core codebase, or forking php - something that can't be done likely. It reads a bit too much like this is something everyone should be doing.