I'm not confident enough to go into the registry and delete things on my own, You could try a registry cleaner. I know a couple for xp but not vista. Windows has an online scan for vista. It might clean it but its a Beta version:
What's new - Windows Live OneCare safety scanner for Windows Vista
When you install another version of LW, it automatically uninstalls your current version. To uninstall manually go to C:\Program Files\LimeWire\Uninstall.exe. Don't use the add/remove programs.
The times I've had trouble connecting after an update have been because of my firewall. Either I've had to make a new exception for LW or java or both. Also check to see that your Listen on Port and PortForward port haven't changed. Open LW and go to Tools>Options>Advanced>FireWall Config, and check the port numbers.