The C:\SmarterMail\Domains folder is not the issue. All the domain files, mailboxes, etc. are installed there and I'm copying the old domain folders to that location. The problem seems to be the 64 bit version of Windows installing all 32 bit programs into the C:\Program Files (x86)\ folder instead of the C:\Program Files\ folder like on the Windows 2003 server.
I have uninstalled SM4, deleted the files from the C:\Program Files (x86)\SmarterTools\SmarterMail\ folder, deleted all SmarterMail registry entries that referenced the (x86) folder and rebooted. I did a fresh install of SM4 and adjusted the installation path to C:\Program Files\SmarterTools\SmarterMail\ , However, after the install completes, I check the folders and find that Windows has still installed it in the (x86) folder. So, therefore, the path will never be identical to the old server.
I can't believe I'm the first person that's had an issue with moving an existing SmarterMail installation from a 32 bit to 64 bit Windows server. Has anyone else had this problem and overcome it?