Hey Dan,
Don't do that. Icoms are much smarter than Yaesus, and allow the computer to initiate the clone. If you put it into clone mode ahead of time, the computer tries to start the clone from scratch and fails. See this in the FAQ:
http://chirp.danplanet.com/projects/chirp/wiki/FAQ#Should-I-put-my-Alinco-Ic...
Hmmm.. then it seems the following "Step 1: Download contents from the radio" section should be amended for Icom users:
http://chirp.danplanet.com/projects/chirp/wiki/Beginners_Guide
Bry: Give Dan's approach a try and see if that changes anything. I also think you should test your cable with shorting the TX to the RX line and use a program like Hyperterminal, etc. to see if you see any typed characters showing up on the screen.
--David