I hate to argue with you Chaz but it's my understanding that the PDC emulation FSMO role is not disabled in a native mode 2000 domain.
Here's a quick bit of info I just found:
http://www.microsoft.com/windows2000/techinfo/reskit/en/distrib/dsbl_fsm_WESD.htm
I have more available in my 2000 Server Resource Kit but I'm not about to start scanning the book when the same info is available on the MS online Res Kit. If you want to learn more on this and other FSMO roles, I recommend going there and reading it.
The PDC emulation FSMO also provides other services like time sync....so disabling it could be problematic.
As to your problem Sam. You should never have an NT PDC running in a 2000 domain. Only BDC's, thus the PDC emulation role. Trying to run a PDC will cause problems and you won't get proper replication from the 2000 DC's and your PDC. If you've physically removed the server and it's "ghost" (for lack of a better term) is still appearing in AD, well, good luck getting rid of it. In fact, if you figure out a way to do this, please let me know as I've encountered this problem on several occasions and have yet to find a resolution. This problem affects domains created then removed as well as servers, clients and other resources listed in the GC in AD. While the ghost shouldn't affect anything adversely (in my experience so far, there have been no adverse side effects from ghosts) it can be annoying and lead to users asking why they can no longer access the now physically removed resource.