Success!!
I have succeeded in getting the examples to work with PHP properly

For those interested here is how I did it...
I used Ant to build the Ajax toolkit and then copied the contents of the Ajax/build/WebRoot directory to my website directory. This copied a across the generated files that where missing. I then converted the JSP pages to PHP and let it run. At this point the examples still didn't work but a little look at the Javascript console told me it couldn't find the AjxCore (plus a few others). Lo and behold the Ajax build folder I copied across only seemed to contain the bits of AjaxTK that it had built and not the core js files etc (I guess they are put in the war file only?).
So I went back to my downloaded source and copied across the directories in Ajax/WebRoot/js. This provided me with the rest of the toolkit and the examples now work as expected.
I hope this help people.
regards,
Jon