If you are having problems with the patch, I have a couple of recommendations off the top of my head. NOTE: I have not installed it yet, and don't know if these will help. Just speaking from experience as a programmer (15 years).
1. I wouldn't try to continue a pre-patch saved game. I would stand up and applaud Firaxis if the patch DID work with a previously saved game. I would suspect some of the issues with commerce getting screwed up, etc. are related to this.
2. If you have made permanent changes to any existing files. Ala Hark's fix (God bless him), I would do a clean install, and then patch. And I know I'm stating the obvious to many, but... make sure you have the latest directX, video drivers, etc.
2b. Not trying to be harsh, but for the dude with Windows Me. STOP BUYING GAMES AND GET XP!!! 'ME' IS CRAP! YOU WILL BE ECSTATICALLY HAPPY THAT YOU DID IT!!! Whew, glad to get that off my chest.
3. Read the README! It has been posted here. It indirectly references the fact that you should not attempt to continue to use Hark's fix among other things.
4. Although I know it pisses you off to install the patch and have things work worse than before on a product you paid good money for, try to be patient. Software is incredibly complex and difficult to develop for the PC (because of all the different possible configurations). This is why the PC game market is shrinking and video games are taking over. Firaxis took a HUGE risk releasing this before Christmas in an attempt to make folks happy. If the patch caused any major regression (which it appears it may have) guess who has to work over the Holidays!
Hope this is helpful! Merry Christmas!
J.