By chance i was faced with a quite similar task some years ago.

I needed to refactor a huge PHP application that was made for parsing and visualizing trace files of a "in-flight multimedia system".

I had the same idea as you and failed.

So i jumped to the conclusion to use a commercial IDE for PHP: NuSphere PhpED.

The software was quite expensive but it "did the job" (bothering through tons of ZEND as well as custom classes.

I hope i understood you right and my suggestion is helpful.