If you deleted the preferences folder, yes that will delete the gnutella.net file also. But next time LW opens it will create a new preferences folder. It should also create a new gnutella.net file 'if' it is able to find the gnutella network.
I'm thinking you might be best port forwarding your Motorolla device. This is not as hard as it sounds, but does require close attention to details.
1. First step is to set up a Static ip address. This is the most important step &
must be done first:
How to set up a static IP address on a Windows Vista
2. Follow directions described here
Port Forwarding Limewire on the Motorola SBG 900. * Might I suggest you choose port 64049 to port forward, not port 21 or 6346 as suggested at the port forward site. You could even use a range of ports; example: start: 6346, end: 65535.
However those two example images at top of the port forward page are for the old LW 4, you can check the ones for LW 5 here:
Manual port forward instructions & sample image (2nd image) But be sure the connection & listening ports for LW in LW's advanced settings match those in the port forwarding of your Motorolla. And it is best if both connection & listening ports are the same.
3. After this entire process, might I suggest you reboot your computer. I'm not sure about your brand of router, but some routers are also best rebooted after making such changes.

Rebooting a router might mean pressing a button in the router's control center that you logged into, or a button on the actual device, or simply turning the power off for a few minutes.