Hi AlecGold.
I honestly think that the s**t is going to hit the fan on this one. Bloggers are all over this and love to tackle Apple on any bona fide issue they can as they don't get too many opportunities like this. So I think that Apple are going to have to cave on this one and you should be able to get a replacement unit if you press them the right way.
Points in your favor:
1. You have a history of Macintosh use which does count for something with these folks.
2. Apple "pushed" this firmware update out by Software Updates which by itself makes them almost wholly responsible for any adverse consequences.
3. The precautionary note provided with the firmware update was very poorly written and the firmware update was probably pushed out too fast with too little thinking about the kinds of scenarios it might face. In this regard, I would STRONGLY suggest that you go to the DL info page and print out a copy before it gets modified or goes missing:
http://support.apple.com/kb/DL853
4. Apple have some explaining to do about why the switched the Nvidia controller to its 1.5 Gbps speed from what previously was set to 3.0 Gbps which in effect constitutes a downgrade from earlier models.
5. In your case you evidently removed the hard drive from an earlier Macbook to install in the new MBP as your old Macbook had problems and the swap out of the drive was performed by an Apple employee (Genius) at an Apple store.
On balance, it looks like you have a very strong case for getting a replacement and Apple are sitting in a bad place. I don't want to knock their Genius crews, but many of them have only been doing this for a year or two and others of us have been doing it for longer than some of these Geniuses have been alive. It really toasts me to have some kid try to put something over on me just to get me out the door.
And yes, I can be verbose. I'm not sorry about that as I learned a long time ago that you need to say enough about these issues to insure that folks don't go out and do the wrong thing because I didn't take the time to adequately address the issues. I think that is what happened to Apple in this case.
I believe that if you line up the info outlined above and call Apple support and tell them that your MBP's controller chip has been fried because of the installation of an Apple supplied drive (albeit from your MB that you are replacing) and cite all of these failings by Apple, then they will do the right thing and replace the unit for you.
Good luck.