I posted this in the 3.0 install guide, but since this is such a common problem, I wanted to post my experience on its own so nobody will miss it:
First of all, thank you very much to everyone for sharing their expertise and experiences. This made things pretty smooth. All in all, this update was a success with my unit (AVIC-F7010BT). I have experienced some of the problems that I see commonly reported here, so I will describe how things went for me...
My unit was recently upgraded to 2.006 (I hope i have the right number of decimal places there) but I had never modded it and I hadn't done anything unofficial with any hack or mod. So I followed the instructions verbatim. When I rebooted, however, I had the system startup message that wouldn't go away. And like so many others, the unit would reboot. This would happen over and over again.
It might be interesting to note that I opened the archives with my Macbook pro. I saw a few posts where this was a concern, and I can add my anecdotal evidence that this may be an issue. I also saw that people have suggested removing everything from MyFlashDisk on the head unit. So, not wanting to have to try everything in "one at a time" fashion, I decided to use Windows to extract the files onto the SD card, and when I copied the files from the dump over the the AVIC-F7010BT, I made sure to delete the MyFlashDisk files first. Luckily, even though I don't have any dedicated Windows machines at home, I have Windows installed in a virtual machine (VMware Fusion).
The conclusion: either extracting and copying the files in Windows, or removing all of the MyFlashDisk files prior to copying (or both of these things) fixed my problem. Now the unit starts up normally and it does not reset after a few minutes.
Please let me know if you have any other questions about my experience with the upgrade. I think I have given you all of the relevant information, but maybe I have missed something that you might be interested in. Anyway, I hope this helps someone else.