Have you tried removing LW rules from your firewall & then adding them again?

I guess you deleted LW's preferences folder? After deleting that folder, did all LW's settings within tools > options revert to default?

Which port is LW currently listening on?

When you updated Java, did you remove any other Java versions installed before installing the update?

AFAIK some Linksys routers aren't reliable in UPnP mode... have you tried port forwarding? The instructions for your router are here: Port Forwarding Limewire on the Linksys WRT54G
First step is to set up a static IP address: PortForward.com - Free Help Setting up Your Router or Firewall

LW's listening port, port in the 'manual port forward' box & port forwarded within router config must all be the same number.