Gregory,
There's no simple way to move your data from 3-Tier to 2-Tier. But you can go from 9.0.118 -> 3-Tier 9.3, you'll just have to upgrade through multiple intermediate versions.
The following gives the overall steps to go from 9.0.161 ->9.3 (you'll have to upgrade 9.0.118 to 9.0.161 first) :
Tech Tip: NFA 9.3.0 Upgrade Path
NFA 9.2 and 9.3 can't be installed on Win2003. Assuming that the existing boxes are Win2003, you can get them up to 9.1.3 then use the following doc to get to NFA 9.2 on a Win2008 VM:
Migrate NFA 9.1.3 Windows 2003 to NFA 9.2 Windows 2008