Hi Allison,
I think you could write a dissertation from everything that's been posted on the forums about the 2000 rev!
I transitioned a year ago and my major issues were with a contract ISO auditor who had only done one previous transition audit and took some very rigid stances on items like 4.2.2 (C), the description of the interaction of processes in the quality manual. Because my manual serves two locations, with differing tier 2 and 3 procedures, I'd made a reference to a tier 2 document in the quality manual to explain the interaction in my division. He took exception to that and insisted that it had to be in the quality manual, not just referenced in the manual.
Some of this auditors findings were later withdrawn by a follow-up auditor as being without merit.
Preparing for the audit was fine. My company has a very mature quality system and good compliance. But auditor interpretations of the language, especially when the standard is new, can throw some curves at you. Some auditors take a very rigid interpretation of the standard, as mine did, and fail to understand that the quality system has to fit the company in order to work well and be of value.