1 how do you tell what port to use?
I think you said you were using Linux. If you're using a USB serial adapter, then you want /dev/ttyUSB0 (assuming you only have one attached). If you're using the first real serial port, then you'll want /dev/ttyS0.
2 How do you set up the radio? I tried turning the rig on while holding down on the left V/M as the book says, but nothing on rig shows "cloning".
You do get the special multi-tone beep and then get dropped into the alternate set menu, right? The cloning mode is the last one in the list, if I recall correctly. That means a single turn to the left will get you there. Then you have to press another button to actually reboot into the cloning menu and then yet another to put it into RX or TX mode.