After doing some searching on google, it turns out that you can run PHP 32 bit on Windows 2003 R2 64 Bit using the FastCGI Extension for IIS 6.0.   Also, using FastCGI is actually faster the the ISAPI dll.  The steps for setting PHP up to use the FastCGI Extension are pretty straight forward.

1. Download & Install the FastCGI Extension for IIS 6.0 from iis.net.  Both 32 bit and 64 are available.
2. Download the latest PHP build from PHP.net
3. Install PHP

During the install, make sure to select IIS FastCGI in the web server setup.

PHP Setup - Web Server Selection

After installing PHP, follow the directions found at:

http://learn.iis.net/page.aspx/247/using-fastcgi-to-host-php-applications-on-iis-60/

I’m seeing great performance running under this setup as well.   Hope this helps you.

Good Reference Sites:

http://devzone.zend.com/article/2710-FastCGI-and-PHP-A-Users-Story

http://blogs.msdn.com/vijaysk/archive/2007/11/16/iis-6-0-fastcgi.aspx

http://mvolo.com/blogs/serverside/archive/2006/09/29/Making-PHP-rock-on-Windows_2F00_IIS.aspx