The problem
is I cannot reproduce the wrong link to /index.
That's not really important, if you solve all the other problems you can leave this one ;-)
I did some exploration of the Go-Pear.php script and I found that in the displayHTMLInstallationSummary() function the $next variable is used for the link that is buggy.
This variable is affected this way :
$next = substr($prefix, strlen($doc_root)).'/index.php';
or
$next = substr($prefix, strlen($file_dir)).'/index.php';
I think the first part is empty, maybe related to the wrong path bug, so only the "/index.php" part remains which cause the bug I experienced.
Hope it helps.
Jean-Marc