That will be kind of difficult as you are changing the architecture the server will be running on.

I'd rather do a fresh install on the VMware machine and migrate the data. You'll avoid many headaches this way

As already stated, the problem is a binary incompatibility one - the actual executables on your IA64 setup will not run on x86_64. If you are using proprietary software on your IA64 setup, you will have to look to see if the license covers reinstalling it, and getting the the correct binaries.
Otherwise,you should be fine just doing a fresh install and choosing the same packages, then migrating the data. This last part shouldn't be too difficult, depending on what you had set up there. All the user files and data will be in /home, so you can just back that up (you can do this just using tar or some desktop backup program) and move it across.
You should also be aware though, that some services (for example mySQL, Apache and practically everything web-based) store their data in different places - usually /var,. So you may need to back up other things too.
Also, and specific configuration files you edited will probably be in /etc
In the case of these last two directories, it isn't a case of just backing them up and dumping them on the new system, because you won't want to overwrite some of the things in the new install, so it's a case of picking through the things you actually need I'm afraid.