After 3 days of trying to do an update, I have some additional information on how to make this work (don't ask me why it didn't work just like it did when I did it earlier -- this is silicon-based life and it's cranky!)
1) Regarding MKISOFS -- it is not included with Cygwin. You have to download it separately and it seems there are several versions around. The one I downloaded is cdrecord for Cygwin available here:
http://smithii.com/?q=node/view/9 I just extracted the files into Cygwin/bin and it worked fine. No error messages.
2) If Mambo comes up on a "site temporarily down" page, Mambo is not talking to the database. I finally fixed this by editing the configuration file to change the database name to '01' like so:
$mosConfig_db= '01';
3) If you have manual links in your website, you will need to edit the database dump to change the paths for those links from "http://mysite.com/" to "http://localhost/"
If you're using 4.5.1, MSAS might be easier....
Good luck!
Susan