In what order do I promote and demote the DC's in a 2000 to 2003 DC replacement?

Since yo already ran adprep your OK there.
Now run dcpromo on the new 2k3 server.  Once its ok then you see replication then transfer all roles to the 2k3 server (FSMO roles) and make the 2k3 machine a global catalog server.
Once done thne you can run a dcpromo on the old machine

So like I said, I've already run the adprep command, but, per instruction from the MS KB, I ran it from the i386 folder on disk 1. The software version of the new DC's is the R2 version. Does this mean I have to run the R2 version or is the adprep version in the i386 folder on disk 1 the same?

You have to run adprep from the r2 disk (second disk)

The R2 version has its own version od ADPREP which you must run instead of the one in the i386 folder, as I said previously the one you want is in the \CMPNENTS\R2\ folder on CD2. Sorry if this was not clear

Okay. So far so good. I just promoted the 2003 DC's successfully into the Domain. I'm at the DNS step. Here is where it gets a little dicey: The DNS on the old servers are not dynamically updating or scavenging and therefore are full of garbage. I would rather start them fresh and leave all of the old config out of it entirely to see if that might fix the issues I can't seem to solve. Is there a way to start a clean DNS server without importing anything from the old DC's that currently are still in the domain?

So when this happens, will the server also copy anything behind the scenes? What I want to avoid here is having it import anything that might be keeping it from dynamically updating and scavenging.