for 2), The usual setting for the OSX firewall, in System Preferences->Sharing->Firewall->New is the "Gnutella/Limewire (6346)." If you are using a different port, like 3643, create a new entry for that port. Really, though, if you are using a router, just turn the OS X firewall off.

for 1)--check the Limewire->Preferences for the shutdown setting. Looks like you want the "shutdown immediately" rather than the "shutdown after transfers are completed" setting.

While you are in the LimeWire Preferences, check out the Bug Reports. In the Example, scroll through the list until you find "Received Incoming this session=TRUE" If it says FALSE", something is still blocking connections which makes uploads difficult.