I've sucessfully finished building the extended CHM.
Good.
About the related bugs:
#25363 is fixed, althought #26311 isn't (the _index.php problem).
I have just fixed #26311. You can replace the script file in the result folder with the new one, and rerun the html help compiler pass to get a corrected file.
#29749 is also not fixed. This is related to some JS problems. I think this is a PhpZ skin specific problem, which is totally broken.
I couldn't fix this because I'm not a js expert. If someone could take a look at this...
What does totally broken mean here? Is it capable of displaying pages on the screen?
Goba