Our organization tried something similar - with just Virusscan 8.7i and AntiSpyware - unsuccessfuly I might add. We were trying to migrate from a Windows Server 2003 x86 machine to Windows Server 2008 Standard R2 x64.
With numerous calls to Mcafee support, the end solution - best soulution, as reccomended by T2 Support, was to completely rebuild it from the ground up. Since x64 machines install 32 bit software to the "Program Files (x86)" directory, and ePo requires the install to be in the same directory on the new server, the end solution was to rebuild from the ground up.
Our organization is small/medium sized (450ish users), and after two weeks, we just wanted to migrate the machine in the quickest way possible - so we decided to stick with a Server 2008 x86 install until McAfee comes up with a way to migrate easily to x64 machines.
Can I ask the reason you need to migrate to a new server/ version?
Just that there may be other solutions, dependent on what your reasons are.
In fact- just noticed this is an old post- Did you find a solutuion?
My organization was getting rid of old hardware - in this case, our ePo server was on an older HP ProLiant DL360 G2 machine (If you're unfamiliar with HP Hardware - These are several years old.) Our focus was to try to migrate everything to newer hardware or VMWare, of which I chose VM.
Server 2008 was the more likely move considering it was supported and we were trying to move whatever we could to it when we had the chance.
Personally, I think Mcafee should note that an x86 to x64 migration is much more different than an x86 to x86 migration - considering even though I mentioned it to T1 during each call for the week or two straight that we were troubleshooting, it was never looked at as a possible problem.
I'm not sure about the original poster however - I just saw it and wanted to respond in case anyone else had similar issues. I saw that it was old, but I figured someone else would want to do this at some point!