Generally speaking Windows Applications must be install from installation media and not just copied from one system to another, physical or virtual. As far as any configuration type files they should be able to be copied, if you know what and where they are. Additionally most Windows programs nowadays store the apps configuration information in the Windows Registry which also can be exported again if you know where to look.
BTW and going forward, It is a known fact that Time Machine is not 100% reliable backing up/restoring Virtual Machines under all circumstances/conditions. Also backing up Virtual Machines via Time Machine is disk/time intensive and wastes a tremendous amount of space for something that may be corrupt and worthless come time to restore it. At a minimum I would exclude Virtual Machines from Time Machine and with the Virtual Machines shutdown, not suspended, and VMware Fusion closed then manually copy the Virtual Machines Package(s) to an alternate location, preferably on to a different physical hard disk. Then keep the User Data that is stored within the Virtual Machine backed up off of the Virtual Machine on a regular basis so as to always have a current User Data Backup. If you have to restore a properly backed up Virtual Machine that is not as current at least you'll have a working Virtual Machine and current User Data to go forward with when you find out your Time Machine Backup of the Virtual Machine fails.
Also have a look at: Best Practices for virtual machine backup (programs and data) in VMware Fusion (1013628)