Yes, I've run the chmod command. I'm asked for password but the terminal doesn't return with anything. The mkdir command is returned with a "mkdir: /var/lock: File exists"
Both makes sense. mkdir tries to create the directory, chmod sets the permissions. chmod would only return something if it failed.
The grep usbmodem isn't returned with anything either even if the UNO is plugged in and blinking away.
lsof stands for "list of open files." grep takes results returned and filters by the keyword. (just running lsof would list *every* open file--keep in mind everything in an UNIX operating system gets a file handle, even devices.) When you get the "Serial port in Use" error, the combination of lsof piped to grep lets you see what processes has the specific serial port open. In your previous case, multiple copies of avrdude were stuck for some reason. -- Note this might have indicated a problem with the 8u2. Look at the forum's sticky posts for a how to do a loop-back test.
The result is still the same: avrdude: stk500_recv(): programmer is not responding
This generic error just tells you that avrdude wasn't able to talk to the programmer. In the case of an arduino, the "programmer" is actually the bootloader on the ATmega328. One reason could be that you've selected the wrong board type (or serial port) in the appropriate drop down menus of the IDE.
How should the UNO look in the System Preferences - Network? Is it enough that it is just there and "not connected". I never got the "pop up" that is described in the manual...
Doesn't matter. It really doesn't matter if it is listed there or not. The Uno emulates an USB Modem, so that no drivers are required. Since it appears to be a modem to OS X, it places an entry in the Network system preferences. All that matters to you / Arduino IDE is that the modem gets assigned a virtual serial port (the tty.usbmodemXXXX name).
Another test might be to run this terminal command with the Uno connected and disconnected:
ls -l /dev/tty.usb*
This will give you an idea what serial port the Uno is being assigned.