As has been suggested before, Use the 6.0 release, it is more secure.
1) Now, what HTML files are you trying to install into the Ibay and are they connected the the index.html file? If you are having problems viewing the HTML files and are receiving some type of access denied or similar error, you may want to check the permission on the files and make sure that they are correctly set for the user and groups you wish access.
2) You could use a link for the index.html file to another file in the same directory or another directory, but remember that if you redirect outside of the IBAY you could run into problems with file permission and users have elevated access. Wouldn't it be easier to change the default web page to be index.html?
3) When you change the PHP.ini file, what is the name of the file that you wish to have processed by php as the default file. If I am not mistaken, php will look for the index.php or index.php3 file to be the default php file in an Ibay.
If you are transfering data from a Windows IIS server, remember that on a *nix system that file names are case sensitive so Index.htnl and index.html are not the same file as they are in Windows.
Darin