You would be better off starting from a fresh install. What doesn't benefit from a fresh windows, but everyone wants to try a p2v right?
If this server has a database, stop it while converting. Or any application that makes a lot of writes for that matter.
Best practices for using and troubleshooting VMware Converter (1004588) http://kb.vmware.com/kb/1004588
Run a chdisk and a sfc scan before converting.
Make sure you have an amazing network connection on layer two to the host from the machine being converted. Routing converter traffic is not a good idea, things tend to break.
As for will it work jumping CPUs....well the window part would. The application....well would that application even work in a virtual environment? If yes, then it likely is written well enough not to want instructions that are vendor specific.